package org.gepard.client.userinterface;
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
import java.io.File;
import java.io.IOException;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.util.Locale;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.ImageIcon;
import javax.swing.InputVerifier;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollBar;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.gepard.client.ClientGlobals;
import org.gepard.client.Config;
import org.gepard.client.Controller;
import org.gepard.client.InvalidParamSetException;
import org.gepard.client.SubstMatrixFile;
import org.gepard.client.SubstMatrixList;
import org.gepard.common.FASTAReader;
import org.gepard.common.InvalidFASTAFileException;
import org.gepard.common.InvalidSubMatFileException;
import org.gepard.common.ParameterSet;
import org.gepard.common.SubstitutionMatrix;
public class ControlPanel extends JPanel implements AdjustmentListener, ActionListener, ChangeListener {
private static final long serialVersionUID = 2211444361988984615L;
private static NumberFormat INTFMT = new DecimalFormat("###,###,###,###,##0", new DecimalFormatSymbols(Locale.ENGLISH));
// main constants
private static final int HOR_MARGIN = 5;
private static final int CMB_HEIGHT = 18;
private static final int SEQ_HEIGHT = 218;
private static final int FUNCT_HEIGHT = 132;
private static final int OPT_HEIGHT = 285;
// sequence tab constants
private static final int SEQ_TAB_SPACE_TOP = 3;
private static final int SEQ_TAB_SPACE_BOTTOM = 3;
private static final int SEQ_TAB_BETWEEN_SEQS = 10;
private static final int SEQ_TAB_INITIAL_TOP = 5;
private static final int SEQ_TAB_BUTTON_HEIGHT = 20;
// function panel
private static final int FUNCT_BETWEEN_ZOOM = 5;
private static final int FUNCT_MARGIN_ZOOM = 10;
private static final int FUNCT_GOADV_HOR_MARGIN = 40;
private static final int FUNCT_ABOVE_GO = 8;
private static final int FUNCT_BELOW_GO = 12;
private static final int FUNCT_ABOVE_ADV = 20;
// plotopt panel
private static final int PLOTOPT_VERTSPACE = 2;
private static final int PLOTOPT_EXTRAVERT = 5;
private static final int PLOTOPT_BEGIN_VERTSPACE = 5;
private static final int PLOTOPT_ITEMS_INDENT = 6;
// misc tab
private static final int MISC_VERTSPACE = 2;
private static final int MISC_EXTRAVERT = 6;
private static final int MISC_INITVERT = 3;
// disp tab
private static final int DISP_VERT_SMALL = 4;
private static final int DISP_VERT_BIG = 8;
private static final int DISP_ABOVE_EXPORT = 5;
// quit button
private static final int QUIT_BTN_HEIGHT = 27;
private static final int BELOW_QUIT_BTN = 5;
private static final int QUIT_BTN_HOR_MARGIN = 40;
// font(s)
private static final Font MAIN_FONT = new Font("Dialog", Font.BOLD, 11);
private static final Font CAPT_FONT = new Font("Dialog", Font.BOLD, 12);
private static final Font TEXT_FONT = new Font("Dialog", Font.PLAIN, 11);
// CONTROLS
// tabs
private JTabbedPane seqTabs;
private JTabbedPane optTabs;
// "Local" tab
private JButton btnLocalSeq1, btnLocalSeq2;
private JTextField txtLocalSeq1, txtLocalSeq2;
private JCheckBox chkFirstComp, chkSecondComp;
// plot options tab
private JCheckBox chkAutoZoom, chkSmallPlots, chkAutoParams, chkAutoMatrix;
private JTextField txtZoom, txtWordlen, txtWinsize;
private CustomComboBox cmbMatrices;
// ... coordinates
private JTextField txtStart1, txtStop1, txtStart2, txtStop2;
// misc tab
private JCheckBox chkSaveSA;
private JLabel lblSASpace;
private JButton btnDeleteSAs;
private JRadioButton optLocalShowAlign, optLocalExport, optLocalDoNothing;
private JButton btnSetupProxy;
// display tab
private JPanel dispTab;
private JScrollBar scrLower, scrUpper, scrGreyscale;// , scrNuclDistr;
private JCheckBox chkRevCompAlign;
// global stuff
private JButton btnGo;
private JButton btnAdvanced;
private JButton btnFullPlot;
private JButton btnZoomOut;
private JButton btnExportFile;
private JButton btnZoomIn;
private JButton btnQuit;
private String curSubmatName;
// current mode (simple or advanced)
private boolean isAdvancedMode = false;
// substitution matrix list
private SubstMatrixFile[] substMatrices;
// custom subst matrix
private SubstitutionMatrix customMatrix = null;
// sequence files changed?
private boolean needreload;
private boolean noScrollbarEvents = false;
// controller object reference
Controller ctrl;
public ControlPanel(Controller ictrl) {
// store controller
ctrl = ictrl;
// load substitution matrices from XML file
try {
substMatrices = SubstMatrixList.getInstance().getMatrixFiles();
} catch (Exception e) {
ClientGlobals.errMessage("Could not open substitution matrix list. " + "The 'matrices/' subfolder seems to be corrupted");
System.exit(1);
}
// sequences panel
JPanel localTab = generateLocalTab();
seqTabs = new JTabbedPane();
// add sequence panes
seqTabs.addTab("Sequences", localTab);
seqTabs.addChangeListener(this);
// function panel
JPanel functPanel = generateFunctionPanel();
// options panel
JPanel plotOptTab = generatePlotOptTab();
JPanel miscTab = generateMiscTab();
dispTab = generateDispTab();
optTabs = new JTabbedPane();
optTabs.setFont(MAIN_FONT);
// optTabs.setBorder(BorderFactory.createEmptyBorder());
optTabs.addTab("Plot", plotOptTab);
optTabs.addTab("Misc", miscTab);
optTabs.addTab("Display", dispTab);
optTabs.setSelectedIndex(0);
// create layout
seqTabs.setAlignmentX(Component.LEFT_ALIGNMENT);
optTabs.setAlignmentX(Component.LEFT_ALIGNMENT);
btnGo.setAlignmentX(Component.LEFT_ALIGNMENT);
functPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
JPanel fixedBox = new JPanel();
fixedBox.setLayout(new BoxLayout(fixedBox, BoxLayout.Y_AXIS));
// fixedBox.setLayout(new GridBagLayout());
fixedBox.add(Box.createRigidArea(new Dimension(0, 3)));
fixedBox.add(seqTabs);
fixedBox.add(Box.createRigidArea(new Dimension(0, 10)));
fixedBox.add(functPanel);
// fixedBox.add(Box.createRigidArea(new Dimension(0,10)));
fixedBox.add(Box.createRigidArea(new Dimension(0, 10)));
fixedBox.add(optTabs);
seqTabs.setPreferredSize(new Dimension(1, SEQ_HEIGHT));
functPanel.setPreferredSize(new Dimension(1, FUNCT_HEIGHT));
optTabs.setPreferredSize(new Dimension(1, OPT_HEIGHT));
// dummy panel which pushes the go button to the bottom of the window
JPanel panelQuit = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = 0;
c.weightx = 1;
c.weighty = 1000;
panelQuit.add(new JLabel(""), c);
c.gridy++;
c.weighty = 1;
c.insets = new Insets(0, HOR_MARGIN + QUIT_BTN_HOR_MARGIN, BELOW_QUIT_BTN, HOR_MARGIN + QUIT_BTN_HOR_MARGIN);
panelQuit.add(btnQuit = new JButton("Quit"), c);
btnQuit.setPreferredSize(new Dimension(1, QUIT_BTN_HEIGHT));
setLayout(new BorderLayout());
add(fixedBox, BorderLayout.NORTH);
add(panelQuit, BorderLayout.CENTER);
btnQuit.addActionListener(this);
// simple or advanced mode
if (Config.getInstance().getIntVal("advanced", 0) == 1)
switchMode(true);
else
switchMode(false);
// help tooltips
btnQuit.setToolTipText(HelpTexts.getInstance().getHelpText("quit"));
// set initial parameters
needreload = true;
setDispTabEnabled(false);
setNavigationEnabled(false);
}
public void setGoButtonCaption(boolean update) {
if (update)
btnGo.setText("Update dotplot");
else
btnGo.setText("Create dotplot");
}
private JPanel generateFunctionPanel() {
HelpTexts hlp = HelpTexts.getInstance();
JPanel functPane = new JPanel();
functPane.setLayout(new GridBagLayout());
// load icons
ImageIcon icoZoomIn = new ImageIcon(this.getClass().getResource("/resources/images/zoomin.gif"));
ImageIcon icoZoomOut = new ImageIcon(this.getClass().getResource("/resources/images/zoomout.gif"));
ImageIcon icoShowFull = new ImageIcon(this.getClass().getResource("/resources/images/zoomfull.gif"));
GridBagConstraints c = new GridBagConstraints();
c.gridx = 0;
c.gridy = 0;
c.weighty = 1;
c.weightx = 1;
c.fill = GridBagConstraints.HORIZONTAL;
c.gridwidth = 4;
c.insets = new Insets(FUNCT_ABOVE_GO, FUNCT_GOADV_HOR_MARGIN, FUNCT_BELOW_GO, FUNCT_GOADV_HOR_MARGIN);
functPane.add(btnGo = getCustomButton(""), c);
c.gridwidth = 1;
c.gridy++;
c.insets = new Insets(0, FUNCT_BETWEEN_ZOOM + FUNCT_MARGIN_ZOOM, 0, FUNCT_BETWEEN_ZOOM);
functPane.add(btnZoomIn = new JButton(icoZoomIn), c);
c.gridx++;
c.insets = new Insets(0, FUNCT_BETWEEN_ZOOM, 0, FUNCT_BETWEEN_ZOOM);
functPane.add(btnZoomOut = new JButton(icoZoomOut), c);
c.gridx++;
functPane.add(btnFullPlot = new JButton(icoShowFull), c);
// advanced mode button
c.insets = new Insets(FUNCT_ABOVE_ADV, FUNCT_GOADV_HOR_MARGIN, 0, FUNCT_GOADV_HOR_MARGIN);
c.gridx = 0;
c.gridy++;
c.gridwidth = 4;
functPane.add(btnAdvanced = getCustomButton(""), c);
setGoButtonCaption(false);
// insert stretcher
c.gridy++;
c.weighty = 10000;
c.gridwidth = 1;
functPane.add(new JLabel(), c);
// event handlers
btnGo.addActionListener(this);
btnAdvanced.addActionListener(this);
btnFullPlot.addActionListener(this);
btnZoomIn.addActionListener(this);
btnZoomOut.addActionListener(this);
// set help texts
btnGo.setToolTipText(hlp.getHelpText("createplot"));
btnZoomIn.setToolTipText(hlp.getHelpText("zoomin"));
btnZoomOut.setToolTipText(hlp.getHelpText("zoomout"));
btnFullPlot.setToolTipText(hlp.getHelpText("fullplot"));
btnAdvanced.setToolTipText(hlp.getHelpText("advmode"));
return functPane;
}
private JPanel generateLocalTab() {
HelpTexts hlp = HelpTexts.getInstance();
JPanel localPanel = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.insets = new Insets(SEQ_TAB_SPACE_TOP + SEQ_TAB_INITIAL_TOP, HOR_MARGIN, SEQ_TAB_SPACE_BOTTOM, HOR_MARGIN);
c.gridx = 0;
c.gridy = 0;
c.gridwidth = 2;
c.gridheight = 1;
c.weightx = 1;
c.weighty = 1;
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
localPanel.add(getLargeLabel("Sequence 1 (horizontal):"), c);
c.insets = new Insets(SEQ_TAB_SPACE_TOP, HOR_MARGIN, SEQ_TAB_SPACE_BOTTOM, HOR_MARGIN);
c.gridy++;
localPanel.add(txtLocalSeq1 = getCustomTextField(""), c);
c.gridy++;
c.gridwidth = 1;
c.gridx = 0;
c.anchor = GridBagConstraints.WEST;
localPanel.add(chkFirstComp = getCustomCheckbox("Complementary"), c);
c.gridx++;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.EAST;
localPanel.add(btnLocalSeq1 = getCustomButton("Select file"), c);
btnLocalSeq1.setPreferredSize(new Dimension(100, SEQ_TAB_BUTTON_HEIGHT));
btnLocalSeq1.setMinimumSize(new Dimension(100, SEQ_TAB_BUTTON_HEIGHT));
c.gridwidth = 2;
c.gridx = 0;
// a little extra space
c.insets = new Insets(SEQ_TAB_SPACE_TOP + SEQ_TAB_BETWEEN_SEQS, HOR_MARGIN, SEQ_TAB_SPACE_BOTTOM, HOR_MARGIN);
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.gridy++;
localPanel.add(getLargeLabel("Sequence 2 (vertical):"), c);
c.insets = new Insets(SEQ_TAB_SPACE_TOP, HOR_MARGIN, SEQ_TAB_SPACE_BOTTOM, HOR_MARGIN);
c.gridy++;
localPanel.add(txtLocalSeq2 = getCustomTextField(""), c);
c.gridy++;
c.gridwidth = 1;
c.gridx = 0;
c.anchor = GridBagConstraints.WEST;
localPanel.add(chkSecondComp = getCustomCheckbox("Complementary"), c);
c.gridx++;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.EAST;
localPanel.add(btnLocalSeq2 = getCustomButton("Select file"), c);
btnLocalSeq2.setPreferredSize(new Dimension(100, SEQ_TAB_BUTTON_HEIGHT));
btnLocalSeq2.setMinimumSize(new Dimension(100, SEQ_TAB_BUTTON_HEIGHT));
// create empty jlabel which eats up the remaining space
c.gridy++;
c.weighty = 200;
localPanel.add(new JLabel(""), c);
// help tooltips
txtLocalSeq1.setToolTipText(hlp.getHelpText("sequence1"));
btnLocalSeq1.setToolTipText(hlp.getHelpText("sequence1select"));
txtLocalSeq2.setToolTipText(hlp.getHelpText("sequence2"));
btnLocalSeq2.setToolTipText(hlp.getHelpText("sequence2select"));
// event handler
btnLocalSeq1.addActionListener(this);
btnLocalSeq2.addActionListener(this);
chkFirstComp.addActionListener(this);
chkSecondComp.addActionListener(this);
return localPanel;
}
private JPanel generatePlotOptTab() {
HelpTexts hlp = HelpTexts.getInstance();
JPanel plotOptTab = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
JLabel horStretcher;
JLabel start1;
c.weightx = 1;
c.weighty = 1;
c.gridx = 0;
c.gridy = 0;
c.fill = GridBagConstraints.HORIZONTAL;
Insets defInsets = new Insets(0, HOR_MARGIN, PLOTOPT_VERTSPACE, HOR_MARGIN);
Insets leftspaceInsets = new Insets(0, HOR_MARGIN + PLOTOPT_ITEMS_INDENT, PLOTOPT_VERTSPACE, HOR_MARGIN);
Insets extraVertInsets = new Insets(0, HOR_MARGIN + PLOTOPT_ITEMS_INDENT, PLOTOPT_VERTSPACE + PLOTOPT_EXTRAVERT, HOR_MARGIN);
c.gridwidth = 2;
c.insets = new Insets(PLOTOPT_BEGIN_VERTSPACE, HOR_MARGIN, PLOTOPT_VERTSPACE, HOR_MARGIN);
plotOptTab.add(getCustomLabel("Coordinates"), c);
c.gridy++;
c.gridwidth = 1;
c.insets = leftspaceInsets;
plotOptTab.add(start1 = getCustomLabel("Start 1:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtStart1 = getCustomTextField("0", 20), c);
c.gridx++;
c.insets = leftspaceInsets;
plotOptTab.add(horStretcher = new JLabel());
c.gridx = 0;
c.gridy++;
c.insets = leftspaceInsets;
plotOptTab.add(getCustomLabel("Stop 1:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtStop1 = getCustomTextField("0", 20), c);
c.gridx = 0;
c.gridy++;
c.insets = leftspaceInsets;
plotOptTab.add(getCustomLabel("Start 2:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtStart2 = getCustomTextField("0", 20), c);
c.gridx = 0;
c.gridy++;
c.insets = extraVertInsets;
plotOptTab.add(getCustomLabel("Stop 2:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtStop2 = getCustomTextField("0", 20), c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
c.insets = defInsets;
plotOptTab.add(chkAutoZoom = getCustomCheckbox("Auto zoom"), c);
c.gridx++;
c.gridwidth = 2;
plotOptTab.add(chkSmallPlots = getCustomCheckbox("Small plots"), c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
c.insets = extraVertInsets;
plotOptTab.add(getCustomLabel("Zoom:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtZoom = getCustomTextField("0", 5), c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 2;
plotOptTab.add(chkAutoParams = getCustomCheckbox("Auto params"), c);
c.gridy++;
c.gridwidth = 1;
c.insets = leftspaceInsets;
plotOptTab.add(getCustomLabel("Word length:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtWordlen = getCustomTextField("10", 5), c);
c.gridx = 0;
c.gridy++;
c.insets = extraVertInsets;
plotOptTab.add(getCustomLabel("Window size:"), c);
c.gridx++;
c.insets = defInsets;
plotOptTab.add(txtWinsize = getCustomTextField("0", 5), c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
plotOptTab.add(chkAutoMatrix = getCustomCheckbox("Auto matrix"), c);
c.gridy++;
c.gridwidth = 1;
c.insets = leftspaceInsets;
plotOptTab.add(getCustomLabel("Use matrix:"), c);
c.gridx++;
c.gridwidth = 2;
c.insets = defInsets;
c.fill = GridBagConstraints.NONE;
c.weighty = 1;
plotOptTab.add(cmbMatrices = getCustomComboBox(), c);
cmbMatrices.setMaximumSize(new Dimension(170, CMB_HEIGHT));
cmbMatrices.setMinimumSize(new Dimension(170, CMB_HEIGHT));
cmbMatrices.setPreferredSize(new Dimension(170, CMB_HEIGHT));
// insert stretcher
c.gridy++;
c.gridx = 0;
c.weighty = 10000;
c.gridwidth = 1;
plotOptTab.add(new JLabel(""), c);
// set sizes
horStretcher.setMinimumSize(new Dimension(50, 1));
start1.setMinimumSize(new Dimension(140, 15));
// help tooltips
chkAutoZoom.setToolTipText(hlp.getHelpText("autozoom"));
txtZoom.setToolTipText(hlp.getHelpText("zoom"));
chkAutoParams.setToolTipText(hlp.getHelpText("autoparams"));
txtWordlen.setToolTipText(hlp.getHelpText("wordlen"));
txtWinsize.setToolTipText(hlp.getHelpText("winsize"));
txtStart1.setToolTipText(hlp.getHelpText("coordinates"));
txtStop1.setToolTipText(hlp.getHelpText("coordinates"));
txtStart2.setToolTipText(hlp.getHelpText("coordinates"));
txtStop2.setToolTipText(hlp.getHelpText("coordinates"));
chkAutoMatrix.setToolTipText(hlp.getHelpText("automatrix"));
cmbMatrices.setToolTipText(hlp.getHelpText("substmatrix"));
chkSmallPlots.setToolTipText(hlp.getHelpText("smallplots"));
// set input verifiers
txtZoom.setInputVerifier(new IntVerifier("Ratio", ClientGlobals.MINZOOM, ClientGlobals.MAXZOOM));
txtWordlen.setInputVerifier(new IntVerifier("Word length", ClientGlobals.MINWORDLEN - 1, ClientGlobals.MAXWORDLEN));
txtWinsize.setInputVerifier(new IntVerifier("Window size", ClientGlobals.MINWINDOWSIZE, ClientGlobals.MAXWINDOWSIZE));
txtStart1.setInputVerifier(new IntVerifier("Coordinates", 0, Integer.MAX_VALUE));
txtStop1.setInputVerifier(new IntVerifier("Coordinates", 0, Integer.MAX_VALUE));
txtStart2.setInputVerifier(new IntVerifier("Coordinates", 0, Integer.MAX_VALUE));
txtStop2.setInputVerifier(new IntVerifier("Coordinates", 0, Integer.MAX_VALUE));
// event handler
chkAutoZoom.addActionListener(this);
chkAutoParams.addActionListener(this);
chkAutoMatrix.addActionListener(this);
cmbMatrices.addActionListener(this);
chkSmallPlots.addActionListener(this);
// read values for auto zoom and auto parameters from config
chkAutoZoom.setSelected(Config.getInstance().getIntVal("autozoom", 1) == 1 ? true : false);
chkAutoParams.setSelected(Config.getInstance().getIntVal("autoparams", 1) == 1 ? true : false);
chkAutoMatrix.setSelected(Config.getInstance().getIntVal("automatrix", 1) == 1 ? true : false);
chkSmallPlots.setSelected(Config.getInstance().getIntVal("smallplots", 0) == 1 ? true : false);
// enable/disable text boxes accordingly
txtZoom.setEnabled(!chkAutoZoom.isSelected());
txtWordlen.setEnabled(!chkAutoParams.isSelected());
txtWinsize.setEnabled(!chkAutoParams.isSelected());
cmbMatrices.setEnabled(!chkAutoMatrix.isSelected());
chkSmallPlots.setEnabled(chkAutoZoom.isSelected());
fillSubstMatrixCombo();
return plotOptTab;
}
private void switchMode(boolean advanced) {
if (advanced) {
btnAdvanced.setText("<< Simple mode");
optTabs.setVisible(true);
isAdvancedMode = true;
} else {
btnAdvanced.setText(">> Advanced mode");
optTabs.setVisible(false);
isAdvancedMode = false;
}
// store setting
Config.getInstance().setIntVal("advanced", isAdvancedMode ? 1 : 0);
}
private void fillSubstMatrixCombo() {
cmbMatrices.removeAllItems();
for (int i = 0; i < substMatrices.length; i++)
// cmbMatrices.addItem("ya");
cmbMatrices.addItem(substMatrices[i].getName());
cmbMatrices.adaptPopupWidth();
}
private JPanel generateMiscTab() {
JPanel miscTab = new JPanel();
HelpTexts hlp = HelpTexts.getInstance();
miscTab.setLayout(new GridBagLayout());
Insets defInsets = new Insets(MISC_VERTSPACE, HOR_MARGIN, 0, HOR_MARGIN);
Insets extraVertInsets = new Insets(MISC_VERTSPACE, HOR_MARGIN, MISC_EXTRAVERT, HOR_MARGIN);
Insets initInsets = new Insets(MISC_VERTSPACE + MISC_INITVERT, HOR_MARGIN, 0, HOR_MARGIN);
GridBagConstraints c = new GridBagConstraints();
c.gridx = 0;
c.gridy = 0;
c.weightx = 1;
c.weighty = 1;
c.anchor = GridBagConstraints.WEST;
c.gridy++;
c.insets = initInsets;
miscTab.add(chkSaveSA = getCustomCheckbox("Save suffix arrays "), c);
c.gridy++;
c.insets = defInsets;
miscTab.add(lblSASpace = getCustomLabel(""), c);
c.gridy++;
c.insets = extraVertInsets;
miscTab.add(btnDeleteSAs = getCustomButton("Delete suffix array files"), c);
c.gridy++;
c.insets = defInsets;
miscTab.add(getCustomLabel("Local dotplot click action..."), c);
c.gridy++;
miscTab.add(optLocalShowAlign = getCustomRadioButton("... show alignment"), c);
c.gridy++;
miscTab.add(optLocalExport = getCustomRadioButton("... export window to FASTA"), c);
c.gridy++;
c.insets = extraVertInsets;
miscTab.add(optLocalDoNothing = getCustomRadioButton("... do nothing"), c);
c.gridy++;
miscTab.add(btnSetupProxy = getCustomButton("HTTP proxy settings"), c);
// set sizes
btnDeleteSAs.setPreferredSize(new Dimension(175, 24));
btnDeleteSAs.setMinimumSize(new Dimension(175, 24));
btnSetupProxy.setPreferredSize(new Dimension(175, 24));
btnSetupProxy.setMinimumSize(new Dimension(175, 24));
// insert stretcher
c.gridy++;
c.weighty = 100000;
c.gridwidth = 1;
miscTab.add(new JLabel(""), c);
updateSADiskSpace();
// pre-select
optLocalShowAlign.setSelected(true);
// create button groups
ButtonGroup localGrp = new ButtonGroup();
localGrp.add(optLocalShowAlign);
localGrp.add(optLocalExport);
localGrp.add(optLocalDoNothing);
// load values from config
chkSaveSA.setSelected(Config.getInstance().getIntVal("savesa", 0) == 1 ? true : false);
optLocalShowAlign.setSelected(Config.getInstance().getIntVal("local_click", 0) == 0 ? true : false);
optLocalExport.setSelected(Config.getInstance().getIntVal("local_click", 0) == 1 ? true : false);
optLocalDoNothing.setSelected(Config.getInstance().getIntVal("local_click", 0) == 2 ? true : false);
// tell GUI if alignments shall be shown (for local plots)
ctrl.showAlignments(optLocalShowAlign.isSelected());
// add action listeners
chkSaveSA.addActionListener(this);
optLocalShowAlign.addActionListener(this);
optLocalExport.addActionListener(this);
optLocalDoNothing.addActionListener(this);
btnDeleteSAs.addActionListener(this);
btnSetupProxy.addActionListener(this);
// help tooltips
chkSaveSA.setToolTipText(hlp.getHelpText("savesa"));
optLocalShowAlign.setToolTipText(hlp.getHelpText("localclick"));
optLocalDoNothing.setToolTipText(hlp.getHelpText("localclick"));
btnDeleteSAs.setToolTipText(hlp.getHelpText("deletesas"));
btnSetupProxy.setToolTipText(hlp.getHelpText("httpproxy"));
return miscTab;
}
private JRadioButton getCustomRadioButton(String caption) {
JRadioButton ret = new JRadioButton(caption);
ret.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
ret.setFont(MAIN_FONT);
return ret;
}
private JCheckBox getCustomCheckbox(String caption) {
JCheckBox ret = new JCheckBox(caption);
ret.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
ret.setFont(MAIN_FONT);
return ret;
}
private JButton getCustomButton(String caption) {
JButton ret = new JButton(caption);
ret.setFont(MAIN_FONT);
return ret;
}
private JLabel getCustomLabel(String caption) {
JLabel ret = new JLabel(caption);
ret.setFont(MAIN_FONT);
return ret;
}
private JLabel getLargeLabel(String caption) {
JLabel ret = new JLabel(caption);
ret.setFont(CAPT_FONT);
return ret;
}
private JTextField getCustomTextField(String text, int size) {
JTextField ret = new JTextField(text, size);
ret.setFont(TEXT_FONT);
return ret;
}
private JTextField getCustomTextField(String text) {
JTextField ret = new JTextField(text);
ret.setFont(TEXT_FONT);
return ret;
}
private CustomComboBox getCustomComboBox() {
CustomComboBox ret = new CustomComboBox();
ret.setFont(TEXT_FONT);
ret.setPreferredSize(new Dimension(1, CMB_HEIGHT));
return ret;
}
private JPanel generateDispTab() {
JPanel dispTab = new JPanel();
HelpTexts hlp = HelpTexts.getInstance();
ImageIcon icoExport = new ImageIcon(this.getClass().getResource("/resources/images/export.gif"));
Insets smallInsets = new Insets(DISP_VERT_SMALL, HOR_MARGIN, 0, HOR_MARGIN);
Insets bigInsets = new Insets(DISP_VERT_BIG, HOR_MARGIN, 0, HOR_MARGIN);
Insets extraInsets = new Insets(DISP_VERT_BIG + DISP_ABOVE_EXPORT, HOR_MARGIN, 0, HOR_MARGIN);
GridBagConstraints c = new GridBagConstraints();
dispTab.setLayout(new GridBagLayout());
c.gridx = 0;
c.gridy = 0;
c.gridwidth = 2;
c.gridheight = 1;
c.weightx = 1;
c.weighty = 1;
c.fill = GridBagConstraints.HORIZONTAL;
c.insets = smallInsets;
dispTab.add(getCustomLabel("Lower color limit:"), c);
c.gridy++;
dispTab.add(scrLower = new JScrollBar(SwingConstants.HORIZONTAL, 0, 0, 0, 1), c);
c.gridy++;
c.insets = bigInsets;
dispTab.add(getCustomLabel("Upper color limit:"), c);
c.gridy++;
c.insets = smallInsets;
dispTab.add(scrUpper = new JScrollBar(SwingConstants.HORIZONTAL, 0, 0, 0, 1), c);
c.gridy++;
c.insets = bigInsets;
dispTab.add(getCustomLabel("Greyscale start:"), c);
c.gridy++;
c.insets = smallInsets;
dispTab.add(scrGreyscale = new JScrollBar(SwingConstants.HORIZONTAL, 0, 0, 0, 100), c);
c.gridy++;
c.insets = bigInsets;
dispTab.add(chkRevCompAlign = getCustomCheckbox("Reverse complementary alignment"), c);
c.gridy++;
c.insets = smallInsets;
c.gridx = 0;
c.gridy++;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.WEST;
c.insets = extraInsets;
c.gridwidth = 1;
dispTab.add(getCustomLabel("Export image:"), c);
c.gridx++;
c.anchor = GridBagConstraints.EAST;
dispTab.add(btnExportFile = new JButton(icoExport), c);
// btnExportFile = new JButton(icoExport);
// insert stretcher
c.gridy++;
c.weighty = 10000;
c.gridwidth = 1;
dispTab.add(new JLabel(), c);
// help tooltips
scrLower.setToolTipText(hlp.getHelpText("lowerlimit"));
scrUpper.setToolTipText(hlp.getHelpText("upperlimit"));
scrGreyscale.setToolTipText(hlp.getHelpText("greyscale"));
btnExportFile.setToolTipText(hlp.getHelpText("export"));
chkRevCompAlign.setToolTipText(hlp.getHelpText("reversecomplementary"));
// add event handler
scrLower.addAdjustmentListener(this);
scrUpper.addAdjustmentListener(this);
scrGreyscale.addAdjustmentListener(this);
btnExportFile.addActionListener(this);
chkRevCompAlign.addActionListener(this);
// set size of export button
btnExportFile.setMaximumSize(new Dimension(20, 30));
return dispTab;
}
private void setDispTabEnabled(boolean e) {
Component[] components = dispTab.getComponents();
for (int i = 0; i < components.length; i++)
components[i].setEnabled(e);
}
private void setNavigationEnabled(boolean e) {
btnZoomOut.setEnabled(e);
btnZoomIn.setEnabled(e);
btnFullPlot.setEnabled(e);
btnExportFile.setEnabled(e);
}
// called by controller when dotplot starts being calculated
public void dotplotStartCalc() {
btnGo.setEnabled(false);
setDispTabEnabled(false);
setNavigationEnabled(false);
}
// called by controller when dotplot is ready
public void dotplotReady() {
btnGo.setEnabled(true);
setDispTabEnabled(true);
setNavigationEnabled(true);
}
// called by controller when dotplot calculation failed
public void dotplotFailed() {
btnGo.setEnabled(true);
if (ctrl.dotplotExists()) {
setDispTabEnabled(true);
setNavigationEnabled(true);
}
// reset coordinates
txtStart1.setText("0");
txtStop1.setText("0");
txtStart2.setText("0");
txtStop2.setText("0");
}
public boolean saveSuffixArrays() {
return chkSaveSA.isSelected();
}
public boolean needReload() {
return needreload;
}
public void setNeedReload(boolean c) {
// set changed flag
needreload = c;
}
// setup scrollbar parameters according to current dotmatrix
public void setupScrollbars(float lowest, float highest) {
noScrollbarEvents = true;
// round limit value
scrLower.setMaximum((int) (highest * 100));
scrUpper.setMaximum((int) (highest * 100));
scrLower.setMinimum((int) (lowest * 100));
scrUpper.setMinimum((int) (lowest * 100));
// set scrollbar increment values
scrLower.setUnitIncrement((int) (highest / 10));
scrLower.setBlockIncrement((int) (highest));
scrUpper.setUnitIncrement((int) (highest / 10));
scrUpper.setBlockIncrement((int) (highest));
noScrollbarEvents = false;
}
public void setScrollbars(float percentLower, float percentUpper, float percentGreyscale, float percentFunCats) {
noScrollbarEvents = true;
// set values
scrUpper.setValue((int) ((float) (scrUpper.getMaximum() - scrUpper.getMinimum()) / 100f * (float) percentUpper) + scrUpper.getMinimum());
scrLower.setValue((int) ((float) (scrLower.getMaximum() - scrLower.getMinimum()) / 100f * (float) percentLower) + scrLower.getMinimum());
scrGreyscale.setValue(
(int) ((float) (scrGreyscale.getMaximum() - scrGreyscale.getMinimum()) / 100f * (float) percentGreyscale) + scrGreyscale.getMinimum());
// manually call adjustment value change handler to invoke
// Plotter.reCalc()
noScrollbarEvents = false;
adjustmentValueChanged(null);
}
public void adjustmentValueChanged(AdjustmentEvent evt) {
try {
if (!noScrollbarEvents) {
// get values
int lv = scrLower.getValue(), uv = scrUpper.getValue(), gv = scrGreyscale.getValue();
// assure lower value is not higher than upper value
if (lv >= uv) {
scrLower.setValue(uv - 1);
lv = uv - 1;
}
// replot
ctrl.eventReplot(lv / 100f, uv / 100f, gv / 100f);
}
} catch (Exception e) {
e.printStackTrace();
ClientGlobals.unexpectedError(e, ctrl);
}
}
public void actionPerformed(ActionEvent evt) {
// catch everything (which is not caught by inner try blocks)
try {
// check which control generated the event
if (evt.getSource() == cmbMatrices) {
// *** MATRIX CHANGED, RELOAD REQUIRED
needreload = true;
// check if the user wants to select a custom matrix file
if (substMatrices[cmbMatrices.getSelectedIndex()].getFile().equals("-")) {
FileChooseResult f = showFileDialog("Select matrix file", true, false);
// set value in GUI
if (f.file != null) {
// try to load this file
try {
customMatrix = SubstitutionMatrix.loadFromFile(f.file);
customMatrix.setNucleotideMatrix(false);
} catch (InvalidSubMatFileException e) {
ClientGlobals.warnMessage("The substitution matrix seems to be invalid.\nPlease specify a matrix file in Blast compatible format.");
customMatrix = null;
}
}
} else
customMatrix = null;
} else if ((evt.getSource() == btnLocalSeq1) || (evt.getSource() == btnLocalSeq2)) {
// *** SELECT SEQUENCE FILE
// show dialog
FileChooseResult f = showFileDialog("Select sequence file", true, false);
// set value in GUI
if (f.file != null) {
if (evt.getSource() == btnLocalSeq1) // set first sequence
txtLocalSeq1.setText(f.file);
else // set second sequence
txtLocalSeq2.setText(f.file);
newDotplot();
}
} else if (evt.getSource() == btnGo) {
initiateLocalDotplot();
} else if (evt.getSource() == chkAutoZoom) {
// *** auto ratio checkbox
// enable/disable ratio text box
txtZoom.setEnabled(!chkAutoZoom.isSelected());
chkSmallPlots.setEnabled(chkAutoZoom.isSelected());
chkSmallPlots.setSelected(false);
// save config setting
Config.getInstance().setVal("autozoom", chkAutoZoom.isSelected() ? "1" : "0");
} else if (evt.getSource() == chkAutoParams) {
// *** auto params checkbox
// enable/disable wordlen & winsize text box
txtWordlen.setEnabled(!chkAutoParams.isSelected());
txtWinsize.setEnabled(!chkAutoParams.isSelected());
// save config setting
Config.getInstance().setVal("autoparams", chkAutoParams.isSelected() ? "1" : "0");
} else if (evt.getSource() == btnFullPlot) {
// *** show full dotplot
ctrl.zoomFullPlot();
} else if (evt.getSource() == btnZoomOut) {
// *** zoom out
ctrl.zoom(ClientGlobals.ZOOMOUTFACTOR);
} else if (evt.getSource() == btnZoomIn) {
// *** zoom in
ctrl.zoom(ClientGlobals.ZOOMINFACTOR);
} else if (evt.getSource() == btnExportFile) {
// *** export image
FileChooseResult f = showFileDialog("Store plot to image file", false, true);
// report to controller
if (f.file != null)
ctrl.eventExportImage(f.file, f.type);
} else if (evt.getSource() == chkSaveSA) {
// save config setting
Config.getInstance().setVal("savesa", chkSaveSA.isSelected() ? "1" : "0");
} else if (evt.getSource() == optLocalShowAlign) {
// tell controller if alignments will be shown
setupForAlignments();
// save setting
Config.getInstance().setVal("local_click", "0");
} else if (evt.getSource() == optLocalExport) {
// tell controller if alignments will be shown
setupForAlignments();
// save setting
Config.getInstance().setVal("local_click", "1");
} else if (evt.getSource() == optLocalDoNothing) {
// tell controller if alignments will be shown
setupForAlignments();
// save setting
Config.getInstance().setVal("local_click", "2");
} else if (evt.getSource() == btnAdvanced)
switchMode(!isAdvancedMode);
else if (evt.getSource() == chkAutoMatrix) {
// set GUI
if (chkAutoMatrix.isSelected()) {
cmbMatrices.setEnabled(false);
cmbMatrices.setSelectedIndex(0);
// store setting
Config.getInstance().setVal("automatrix", "1");
} else {
cmbMatrices.setEnabled(true);
// store setting
Config.getInstance().setVal("automatrix", "0");
}
} else if (evt.getSource() == btnDeleteSAs) {
// delete suffix array files
deleteSAFiles();
updateSADiskSpace();
} else if (evt.getSource() == btnQuit) {
ctrl.exit();
} else if (evt.getSource() == btnSetupProxy) {
new ProxyDialog(ctrl);
} else if (evt.getSource() == chkSmallPlots) {
// store setting
Config.getInstance().setVal("smallplots", (chkSmallPlots.isSelected()) ? "1" : "0");
} else if (evt.getSource() == chkFirstComp) {
if (chkFirstComp.isSelected())
chkSecondComp.setSelected(false);
newDotplot();
} else if (evt.getSource() == chkSecondComp) {
if (chkSecondComp.isSelected())
chkFirstComp.setSelected(false);
newDotplot();
} else if (evt.getSource() == chkRevCompAlign) {
ctrl.updateAlignment();
}
} catch (Exception e) {
e.printStackTrace();
ClientGlobals.unexpectedError(e, ctrl);
}
}
private void setupForAlignments() {
// local mode
if (optLocalShowAlign.isSelected())
ctrl.showAlignments(true);
else
ctrl.showAlignments(false);
}
private void newDotplot() {
// set changed flag
needreload = true;
// set coordinates to zero
txtStart1.setText("0");
txtStop1.setText("0");
txtStart2.setText("0");
txtStop2.setText("0");
// set go-button caption
setGoButtonCaption(false);
}
private void initiateLocalDotplot() {
// check if the user actually selected two sequences
if (txtLocalSeq1.getText().trim().equals("") || txtLocalSeq2.getText().trim().equals("")) {
ClientGlobals.warnMessage("Please select two sequence files.");
return;
}
// determine type of both sequence files
boolean firstSecIsNucl;
try {
firstSecIsNucl = FASTAReader.isNucleotideFile(txtLocalSeq1.getText());
} catch (IOException e) {
ClientGlobals.errMessage("Failed loading sequence file 1\nIO error: " + e.getMessage());
return;
} catch (InvalidFASTAFileException e) {
ClientGlobals.errMessage("Failed loading sequence file 1\nInvalid FASTA file: " + e.getMessage());
return;
}
boolean secondSecIsNucl;
try {
secondSecIsNucl = FASTAReader.isNucleotideFile(txtLocalSeq2.getText());
} catch (IOException e) {
ClientGlobals.errMessage("Failed loading sequence file 2\nIO error: " + e.getMessage());
return;
} catch (InvalidFASTAFileException e) {
ClientGlobals.errMessage("Failed loading sequence file 2\nInvalid FASTA file: " + e.getMessage());
return;
}
// load matrix
String basePath = ClientGlobals.PATH_MATRICES;
SubstitutionMatrix mat;
if (!chkAutoMatrix.isSelected()) {
// no automatrix-mode
if (customMatrix == null) {
// use specified matrix
mat = loadSubstMatrix(basePath + substMatrices[cmbMatrices.getSelectedIndex()].getFile());
mat.setNucleotideMatrix(substMatrices[cmbMatrices.getSelectedIndex()].isNucleotideMatrix());
curSubmatName = substMatrices[cmbMatrices.getSelectedIndex()].getName();
} else {
// use custom matrix
mat = customMatrix;
curSubmatName = "Custom";
}
// one cannot use custom DNA substitution matrices
if (customMatrix != null && (firstSecIsNucl || secondSecIsNucl)) {
ClientGlobals.warnMessage("Custom matrices are only allowed for protein dotplots.");
return;
}
} else {
// auto-matrix mode
// check if both types are equal
if (firstSecIsNucl != secondSecIsNucl) {
ClientGlobals.warnMessage("The two sequences do not seem to have the same type (DNA/Protein).\n"
+ "Please choose different sequences or do not use auto-matrix mode.");
return;
}
// now set automatic matrix
if (firstSecIsNucl) {
mat = loadSubstMatrix(basePath + ClientGlobals.AUTO_NUCL_MATRIX);
curSubmatName = ClientGlobals.AUTO_NUCL_MATRIX_NAME;
mat.setNucleotideMatrix(true);
} else {
mat = loadSubstMatrix(basePath + ClientGlobals.AUTO_PROT_MATRIX);
curSubmatName = ClientGlobals.AUTO_PROT_MATRIX_NAME;
mat.setNucleotideMatrix(false);
}
}
// get parameters
ParameterSet params;
try {
params = getParameterSet(false);
} catch (InvalidParamSetException e) {
// do nothing, getParameterSet() has already informed the user
return;
}
if (params == null) {
dotplotFailed();
return;
}
// do last GUI check
if ((params.wordLength == 0) && (params.windowSize == 0)) {
ClientGlobals.warnMessage("Whether window size or word length must have a non-zero value");
return;
}
if (mat != null) {
// determine if theres a sequence we need to use the complementary
// of
int compseq = 0;
if (chkFirstComp.isSelected())
compseq = 1;
if (chkSecondComp.isSelected())
compseq = 2;
// create local dotplot
ctrl.initiateLocalDotplot(mat, txtLocalSeq1.getText(), txtLocalSeq2.getText(), params, compseq);
}
}
public ParameterSet getParameterSet(boolean novalidation) throws InvalidParamSetException {
// read values
try {
int ratio = Integer.parseInt(txtZoom.getText());
int wordlen = Integer.parseInt(txtWordlen.getText());
int windowsize = Integer.parseInt(txtWinsize.getText());
int seq1start = Integer.parseInt(txtStart1.getText());
int seq1stop = Integer.parseInt(txtStop1.getText());
int seq2start = Integer.parseInt(txtStart2.getText());
int seq2stop = Integer.parseInt(txtStop2.getText());
// parameter validation
if (!novalidation
&& (((seq1stop <= seq1start) && (seq1start != 0 || seq1stop != 0)) || ((seq2stop <= seq2start) && (seq2start != 0 || seq2stop != 0)))) {
ClientGlobals.warnMessage("Sequence start parameter must be smaller than stop parameter");
throw new InvalidParamSetException();
}
// return parameter set
return new ParameterSet(ratio, wordlen, windowsize, seq1start, seq1stop, seq2start, seq2stop, curSubmatName);
} catch (Exception e) {
// we need to catch an exception here as GUI values became corrupted
// sometimes
ClientGlobals.warnMessage("Something went wrong in the GUI, please try again what you were just intending to do.");
e.printStackTrace();
return null;
}
}
public void setParameterSet(ParameterSet params) {
// set values
txtZoom.setText(params.zoom + "");
txtWordlen.setText(params.wordLength + "");
txtWinsize.setText(params.windowSize + "");
txtStart1.setText(params.seq1Start + "");
txtStop1.setText(params.seq1Stop + "");
txtStart2.setText(params.seq2Start + "");
txtStop2.setText(params.seq2Stop + "");
}
public boolean useAutoZoom() {
return chkAutoZoom.isSelected();
}
public boolean useAutoParameters() {
return chkAutoParams.isSelected();
}
public void showOptionsTab() {
optTabs.setSelectedIndex(0);
}
public void showDisplayTab() {
optTabs.setSelectedIndex(2);
}
public int getLocalClickAction() {
if (optLocalShowAlign.isSelected())
return ClientGlobals.LOCALCLICK_SHOWALIGN;
else if (optLocalExport.isSelected())
return ClientGlobals.LOCALCLICK_EXPORT;
else
return ClientGlobals.LOCALCLICK_NOTHING;
}
private FileChooseResult showFileDialog(String title, boolean open, boolean imageexport) {
// create file chooser object
JFileChooser f;
if (!imageexport)
f = new JFileChooser(Config.getInstance().getStringVal("lastopendir", ""));
else
f = new JFileChooser(Config.getInstance().getStringVal("lastopendir_export", ""));
if (imageexport) {
// remove first filter
f.removeChoosableFileFilter(f.getFileFilter());
ExampleFileFilter filter = new ExampleFileFilter();
filter.addExtension("jpg");
filter.addExtension("jpeg");
filter.setDescription("JPEG image files");
f.addChoosableFileFilter(filter);
filter = new ExampleFileFilter();
filter.addExtension("png");
filter.setDescription("PNG image files");
f.addChoosableFileFilter(filter);
filter = new ExampleFileFilter();
filter.addExtension("bmp");
filter.setDescription("Bitmap image files");
f.addChoosableFileFilter(filter);
}
// show correct dialog
int retval;
if (open)
retval = f.showOpenDialog(this);
else
retval = f.showSaveDialog(this);
if (retval == JFileChooser.APPROVE_OPTION && f.getSelectedFile() != null) {
// store dir
if (!imageexport)
Config.getInstance().setVal("lastopendir", f.getSelectedFile().getParent());
else
Config.getInstance().setVal("lastopendir_export", f.getSelectedFile().getParent());
String filename = f.getSelectedFile().getAbsolutePath();
String selextension;
// append extension if needed and if in image mode
if (imageexport) {
// get extension of selected type
ExampleFileFilter sel = (ExampleFileFilter) f.getFileFilter();
selextension = sel.getFirstExtension();
// if this is a save file dialog and the entered file name
// does not have an extension -> add extension
if (!open && (filename.lastIndexOf(".") == -1))
filename += "." + selextension;
} else
selextension = "";
// return filename and type
return new FileChooseResult(filename, selextension);
} else
return new FileChooseResult(null, null);
}
private SubstitutionMatrix loadSubstMatrix(String file) {
// call static load method
try {
SubstitutionMatrix mat = SubstitutionMatrix.loadFromResource(file);
return mat;
} catch (IOException e) {
JOptionPane.showMessageDialog(null, "IO error while opening matrix file:\n" + e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
return null;
} catch (InvalidSubMatFileException e) {
//
JOptionPane.showMessageDialog(null, "Could not load matrix file:\n" + e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
return null;
}
}
class IntVerifier extends InputVerifier {
private String m_name;
private int m_min, m_max;
public IntVerifier(String name, int min, int max) {
m_name = name;
m_min = min;
m_max = max;
}
public boolean verify(JComponent input) {
// get text
String contents = ((JTextField) input).getText();
// assume valid input
boolean valueok = true;
// check if text field contains a valid integer between m_min and
// m_max
try {
int value = Integer.parseInt(contents);
if ((value < m_min) || (value > m_max))
valueok = false;
} catch (NumberFormatException nfe) {
valueok = false;
}
if (valueok == false)
// show warning message
JOptionPane.showMessageDialog(input.getParent().getParent(),
m_name + " must be a valid integer between " + INTFMT.format(m_min) + " and " + INTFMT.format(m_max), "Invalid value",
JOptionPane.WARNING_MESSAGE);
return valueok;
}
}
private class FileChooseResult {
public String file;
public String type;
public FileChooseResult(String file, String type) {
this.file = file;
this.type = type;
}
}
private long calcCurrentSADiskSpace() {
long totalSize = 0;
// iterate over file list
String[] saFiles = new File(ClientGlobals.SETTINGS_DIR).list();
for (int i = 0; i < saFiles.length; i++) {
// check for .sa extension
if (saFiles[i].substring(saFiles[i].length() - 3).equals(".sa"))
totalSize += new File(ClientGlobals.SETTINGS_DIR + System.getProperty("file.separator") + saFiles[i]).length();
}
return totalSize;
}
private void deleteSAFiles() {
// iterate over file list
String[] saFiles = new File(ClientGlobals.SETTINGS_DIR).list();
for (int i = 0; i < saFiles.length; i++) {
// check for .sa extension
if (saFiles[i].substring(saFiles[i].length() - 3).equals(".sa"))
new File(ClientGlobals.SETTINGS_DIR + System.getProperty("file.separator") + saFiles[i]).delete();
}
}
public void updateSADiskSpace() {
lblSASpace.setText("Suffix arrays diskspace: " + ClientGlobals.convenientFileSize(calcCurrentSADiskSpace()));
}
public void stateChanged(ChangeEvent arg0) {
// disable funcat tab in local mode
optTabs.setEnabledAt(3, seqTabs.getSelectedIndex() == 1);
setupForAlignments();
}
public boolean smallPlots() {
return chkSmallPlots.isSelected();
}
public void uncheckFirstComp() {
chkFirstComp.setSelected(false);
}
public void uncheckSecondComp() {
chkSecondComp.setSelected(false);
}
public String getGUIDump() {
StringBuilder guidump = new StringBuilder();
// local sequences
guidump.append("==== LOCAL SEQUENCES ====\n");
guidump.append("Sequence 1: " + this.txtLocalSeq1.getText() + "\n");
guidump.append("Seq1comp : " + this.chkFirstComp.isSelected() + "\n");
guidump.append("Sequence 2: " + this.txtLocalSeq2.getText() + "\n");
guidump.append("Seq2comp : " + this.chkSecondComp.isSelected() + "\n");
guidump.append("\n");
// plot settings
guidump.append("==== PLOT SETTINGS ====\n");
guidump.append("Seq1 coords : " + this.txtStart1.getText() + "-" + this.txtStop1.getText() + "\n");
guidump.append("Seq2 coords : " + this.txtStart2.getText() + "-" + this.txtStop2.getText() + "\n");
guidump.append("Auto zoom : " + this.chkAutoZoom.isSelected() + "\n");
guidump.append("Small plots: " + this.chkSmallPlots.isSelected() + "\n");
guidump.append("Zoom : " + this.txtZoom.getText() + "\n");
guidump.append("Auto params : " + this.chkAutoParams.isSelected() + "\n");
guidump.append("Word length : " + this.txtWordlen.getText() + "\n");
guidump.append("Window size : " + this.txtWinsize.getText() + "\n");
guidump.append("Auto matrix: " + this.chkAutoMatrix.isSelected() + "\n");
guidump.append("Matrix : " + this.cmbMatrices.getSelectedItem() + "\n");
guidump.append("\n");
// misc settings
guidump.append("==== MISC SETTINGS ====\n");
guidump.append("Save SAs: " + this.chkSaveSA.isSelected() + "\n");
String localaction;
if (this.optLocalDoNothing.isSelected())
localaction = "Do nothing";
else
localaction = "Show alignment";
guidump.append("Local click action: " + localaction + "\n");
guidump.append("\n");
return guidump.toString();
}
public void setRevComplAlign(boolean revcomp) {
chkRevCompAlign.setSelected(revcomp);
}
public boolean reverseComplementaryAlignments() {
return chkRevCompAlign.isSelected();
}
public void setNucleotidePlot(boolean nuclplot) {
if (nuclplot) {
chkRevCompAlign.setEnabled(true);
} else {
chkRevCompAlign.setEnabled(false);
chkRevCompAlign.setSelected(false);
}
}
}
