Java Code Examples for java.util.LinkedHashMap#keySet()

The following examples show how to use java.util.LinkedHashMap#keySet() . These examples are extracted from open source projects. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source Project: singleton   File: SignatureUtil.java    License: Eclipse Public License 2.0 6 votes vote down vote up
/**
 * A helper util for generate signature
 *
 * @param paramMap The parameters for generation signature
 * @return signature string
 */
public static String sign(LinkedHashMap<String, String> paramMap) {
    if (null == paramMap) {
        throw new RuntimeException("signature parameter can't null");
    }
    StringBuilder paramStr = new StringBuilder();
    for (String key : paramMap.keySet()) {
        paramStr.append(key);
        paramStr.append(paramMap.get(key));
    }
    try {
        String signatureStr = EncryptUtil.SHA512(paramStr.toString().getBytes(
                ConstantsUnicode.UTF8));
        return signatureStr.toUpperCase();
    } catch (UnsupportedEncodingException e) {
    	logger.error(e.getMessage(), e);
    }
    return "";
}
 
Example 2
public void registerPatternBlocks(final Map<String, String[]> patternBlocks)
		throws GrokException {
	HashMap<String, String> groupMapping = new HashMap<String, String>();
	LinkedHashMap<String, String> strPatterns = new LinkedHashMap<String, String>();
	for (String group : patternBlocks.keySet()) {
		grokGroups.put(group, new LinkedHashMap<String, Grok>());
		for (String block : patternBlocks.get(group)) {
			for (String line : block.split("\n")) {
				Matcher m = PATTERN_ENTRY.matcher(line);
				if (m.matches()) {
					strPatterns.put(m.group(1), m.group(2));
					groupMapping.put(m.group(1), group);
				}
			}
		}
	}
	for (String name : new ArrayList<String>(strPatterns.keySet())) {
		// Could be already compiled by sub reference
		if (strPatterns.containsKey(name)) {
			compile(name, strPatterns.get(name), strPatterns, groupMapping);
		}
	}
	logger.info("Registered grok patterns: {}", groks.keySet());
}
 
Example 3
Source Project: chipster   File: ToolUtils.java    License: MIT License 6 votes vote down vote up
/**
 * 
 * Write additional information about input datasets to a file
 * 
 * @param file
 * @param nameMap
 * @throws IOException 
 */
public static void writeInputDescription(File file, LinkedHashMap<String, String> nameMap) throws IOException {
	
	try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
		writer.write("# Chipster dataset description file\n");
		writer.write("# \n");
		writer.write("# Additional columns may be added later, so don't assume that there will be only two of them.\n");
		writer.write("# Comment lines are allowed only in the beginning of file, but the number of them may vary.\n");
		writer.write("# Avoid using dataset names as file names on the server side, although those go through a cursory sanitization.\n");
		writer.write("# \n");
		writer.write("# INPUT_NAME	DATASET_NAME\n");
		
		for (String input : nameMap.keySet()) {
			String name = nameMap.get(input);
			if (name == null) {
				throw new IllegalArgumentException("Dataset name of input '" + input + "' is null. Please rename the dataset.");
			}
			if (!name.matches(NAME_PATTERN)) {
				throw new IllegalArgumentException("Dataset name " + name + " contains illegal characters. Please rename the dataset.");
			}
			writer.write(input + "\t" + name + "\n");
		}
	}
}
 
Example 4
/**
 * This function gets all the best time windows from spectra in water and meoh media, so that they can analyzed
 * by the yeast media samples for snr analysis.
 * @param waterAndMeohSpectra A list of ions to best XZ value.
 * @return A map of ion to list of restricted time windows.
 */
public static Map<String, List<Double>> getRestrictedTimeWindowsForIonsFromWaterAndMeOHMedia(
    List<LinkedHashMap<String, XZ>> waterAndMeohSpectra) {

  Map<String, List<Double>> ionToRestrictedTimeWindows = new HashMap<>();

  for (LinkedHashMap<String, XZ> entry : waterAndMeohSpectra) {
    for (String ion : entry.keySet()) {
      List<Double> restrictedTimes = ionToRestrictedTimeWindows.get(ion);
      if (restrictedTimes == null) {
        restrictedTimes = new ArrayList<>();
        ionToRestrictedTimeWindows.put(ion, restrictedTimes);
      }
      Double timeValue = entry.get(ion).getTime();
      restrictedTimes.add(timeValue);
    }
  }

  return ionToRestrictedTimeWindows;
}
 
Example 5
private Map<String, String> getOwnershipMap() {
	Map<String, String> ownershipMap = null;

	try {
		ObjectName mObjNameStorageService = new ObjectName(
				CassandraConstants.ORG_APACHE_CASSANDRA
						+ "db:type="
						+ CassandraConstants.Cassandra_JMX_Attributes.CASSANDRA_JMX_OBJECT_STORAGESERVICE);

		Object attrOwnership = jmxUtil
				.getAttribute(
						mObjNameStorageService,
						CassandraConstants.Cassandra_JMX_Attributes.CASSANDRA_JMX_ATTRIBUTE_OWNERSHIP);
		LinkedHashMap ownership = (LinkedHashMap) attrOwnership;

		ownershipMap = new HashMap<String, String>();
		for (Object key : ownership.keySet()) {
			ownershipMap
					.put(key.toString().substring(
							key.toString().lastIndexOf("/") + 1),
							String.valueOf(df.format(((Float) ownership
									.get(key)) * 100)) + " %");
		}

	} catch (MalformedObjectNameException e) {
		LOG.error("Could not get ownership details.", e);
	}

	return ownershipMap;
}
 
Example 6
Source Project: JZVideoDemo   File: JZUtils.java    License: MIT License 5 votes vote down vote up
public static Object getValueFromLinkedMap(LinkedHashMap<String, Object> map, int index) {
    int currentIndex = 0;
    for (String key : map.keySet()) {
        if (currentIndex == index) {
            return map.get(key);
        }
        currentIndex++;
    }
    return null;
}
 
Example 7
Source Project: JZVideoDemo   File: JZUtils.java    License: MIT License 5 votes vote down vote up
public static String getKeyFromDataSource(Object[] dataSourceObjects, int index) {
    LinkedHashMap<String, Object> map = (LinkedHashMap) dataSourceObjects[0];
    int currentIndex = 0;
    for (String key : map.keySet()) {
        if (currentIndex == index) {
            return key;
        }
        currentIndex++;
    }
    return null;
}
 
Example 8
@Test(dataProvider = "getRenameCombinations")
public void testRenamingSamples(final Map<String, String> renamingMap, final int threads, final int batchSize) throws IOException {
    final LinkedHashMap<String, String> sampleMap = new LinkedHashMap<>(renamingMap);
    sampleMap.replaceAll( (newSampleName, originalSampleName)-> createInputVCF(originalSampleName).getAbsolutePath());

    final File sampleMapFile = getSampleMapFile(sampleMap);

    final String workspace = createTempDir("workspace").getAbsolutePath();
    Files.delete(Paths.get(workspace));
    final ArgumentsBuilder args = new ArgumentsBuilder()
            .add(GenomicsDBImport.SAMPLE_NAME_MAP_LONG_NAME, sampleMapFile.getAbsolutePath())
            .add(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, new File(workspace).getAbsolutePath())
            .add(GenomicsDBImport.VCF_INITIALIZER_THREADS_LONG_NAME, String.valueOf(threads))
            .add(GenomicsDBImport.BATCHSIZE_ARG_LONG_NAME, String.valueOf(batchSize))
            .addInterval(INTERVAL.get(0));

    runCommandLine(args);
    final Set<String> expectedSampleNames = sampleMap.keySet();
    try(final FeatureReader<VariantContext> reader = getGenomicsDBFeatureReader(workspace, b37_reference_20_21)) {
        final CloseableTribbleIterator<VariantContext> iterator = reader.iterator();
        Assert.assertTrue(iterator.hasNext(), "expected to see a variant");
        Assert.assertTrue(expectedSampleNames.size() > 0);
        Assert.assertEquals(expectedSampleNames.size(), renamingMap.size());
        iterator.forEachRemaining(vc -> {
            Assert.assertEquals(vc.getSampleNames().size(), expectedSampleNames.size());
            Assert.assertEqualsNoOrder(vc.getSampleNames().toArray(), expectedSampleNames.toArray());
            expectedSampleNames.forEach( sample -> {
                Assert.assertEquals(vc.getGenotype(sample).getAnyAttribute(SAMPLE_NAME_KEY), renamingMap.get(sample));
                //check another attribute just to make sure we're not mangling things
                Assert.assertEquals(VariantContextGetters.getAttributeAsInt(vc.getGenotype(sample), ANOTHER_ATTRIBUTE_KEY, -1), 10);
            });
        });
    }

}
 
Example 9
Source Project: apogen   File: Jaccard.java    License: Apache License 2.0 5 votes vote down vote up
public static LinkedHashMap<Integer, LinkedList<String>> cleanMap(LinkedHashMap<Integer, LinkedList<String>> map) {

		LinkedHashMap<Integer, LinkedList<String>> output = new LinkedHashMap<Integer, LinkedList<String>>();

		int i = 0;
		for (Integer c : map.keySet()) {
			if (!map.get(c).isEmpty()) {
				output.put(i, map.get(c));
				i++;
			}
		}

		return output;
	}
 
Example 10
private TableEntry getTableEntry(String tableName, LinkedHashMap<String, String> tableOptions){
    final TableEntry detector = new TableEntry();
    detector.setTableName(tableName);
    for (String tableHead: tableOptions.keySet()) {
        detector.getTableHead().getRow().addCell(new TableCellEntry(tableHead));
    }
    TableRowEntry row = contructRow(tableOptions.values());
    detector.getTableBody().addRow(row);

    return detector;
}
 
Example 11
Source Project: helix   File: TestAutoRebalanceStrategy.java    License: Apache License 2.0 5 votes vote down vote up
/**
 * Get a StateModelDefinition without transitions. The auto rebalancer doesn't take transitions
 * into account when computing mappings, so this is acceptable.
 * @param modelName name to give the model
 * @param initialState initial state for all nodes
 * @param states ordered map of state to count
 * @return incomplete StateModelDefinition for rebalancing
 */
private StateModelDefinition getIncompleteStateModelDef(String modelName, String initialState,
    LinkedHashMap<String, Integer> states) {
  StateModelDefinition.Builder builder = new StateModelDefinition.Builder(modelName);
  builder.initialState(initialState);
  int i = states.size();
  for (String state : states.keySet()) {
    builder.addState(state, i);
    builder.upperBound(state, states.get(state));
    i--;
  }
  return builder.build();
}
 
Example 12
/**
 * If any not numeric value then categorical
 * @param values
 * @return
 */
private static boolean isCategorical(LinkedHashMap<String, Double> values) {
	try {
		for (String value : values.keySet()) {
			Double.parseDouble(value);
		}
		return false;
	} catch (Exception e) {
		return true;
	}

}
 
Example 13
/**
 * 从标准行情数据目录导入
 */
private void importFromDataDir() throws Exception
{
    File marketData = TraderHomeUtil.getDirectory(TraderHomeUtil.DIR_MARKETDATA);
    File trashDir = TraderHomeUtil.getDirectory(TraderHomeUtil.DIR_TRASH);

    writer.println("从行情数据目录导入: "+marketData.getAbsolutePath());writer.flush();
    for(File tradingDayDir: FileUtil.listSubDirs(marketData)) {
        LocalDate date = DateUtil.str2localdate(tradingDayDir.getName());
        if ( date==null ) {
            writer.println("忽略目录 "+tradingDayDir);
            continue;
        }
        writer.print("导入交易日 "+tradingDayDir.getName()+" :"); writer.flush();
        LinkedHashMap<Exchangeable, List<MarketDataInfo>> marketDataInfos = loadMarketDataInfos(tradingDayDir);
        List<Exchangeable> exchangeables = new ArrayList<>(marketDataInfos.keySet());
        Collections.sort(exchangeables);
        for(Exchangeable e:exchangeables) {
            //为每个品种找到最合适的文件
            List<MarketDataInfo> mdInfos = marketDataInfos.get(e);
            Collections.sort(mdInfos);
            //实际导入
            MarketDataInfo mdInfo = mdInfos.get(mdInfos.size()-1);
            importMarketData(date, mdInfo);
            writer.print(" "+mdInfo.exchangeable+"("+mdInfo.savedTicks+"/"+mdInfo.tickCount+")"); writer.flush();
        }
        writer.println();
        //将每日目录转移trash目录中
        if ( moveToTrash ) {
            moveToTrash(trashDir, tradingDayDir);
        }
    }
}
 
Example 14
/**
 * Create a key including the
 * <li><b>expenditureFinancialDocumentNumber</b></li>
 * <li><b>expenditureFinancialDocumentTypeCode</b></li>
 * with accounting information for asset payment distribution
 *
 * Make sure the full accounting line information is part of the key
 * chartOfAccount, accountNumber, subAccountNumber, objectCode, subObjectCode, projectCode
 *
 * @return
 */
public String getAssetPaymentDetailKey() {
    LinkedHashMap<String,String> paymentMap = assetPaymentToStringMapper();
    paymentMap.put("expenditureFinancialDocumentTypeCode",this.getExpenditureFinancialDocumentTypeCode());
    paymentMap.put("expenditureFinancialDocumentNumber",this.getExpenditureFinancialDocumentNumber());

    //use SHORT_PREFIX_STYLE so that memory address is not part of the toString output
    ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
    for (String key : paymentMap.keySet()){
        builder.append(key, paymentMap.get(key));
    }
    return paymentMap.toString();
}
 
Example 15
/**
 * Creates various extra statements that we need.
 * <p/>
 * One of these is to create a constraint_failure() procedure, since MySQL has
 * no way to abort a transaction other than performing an invalid query
 * (constraint_failure() attempts an "UPDATE" of "fail = 1" on a table named
 * whatever failure message is passed in; that way at least the error appears in
 * the MySQL error message. This sucks, I know. Blame MySQL.)
 * <p/>
 * FIXME: Right now, MySQL <b>does not support</b> updating the same table a
 * trigger applies to in an AFTER trigger, so we have no way to clear shadow
 * columns. This was presumably a result of MySQL incompetence, or MySQL's
 * philosophy of limiting itself in order to prevent idiot PHP programmers from
 * shooting themselves in the foot with--*GASP*--a recursive trigger. While it
 * would be very nice to clear the shadow columns, we simply can't do so: the
 * values are often needed in AFTER INSERT or AFTER UPDATE triggers, so we can't
 * clear them before then, however the only entry point for clearing these with
 * MySQL is doing a 'SET NEW.col = NULL' inside the BEFORE trigger.
 * <p/>
 * If MySQL some day supports an update on the same table a trigger is applied
 * to, the following will work. Until then, MySQL tables will end up retaining
 * values in the shadow columns. N.B. that these values are actual references to
 * the appropriate tables and columns, but are 'ON DELETE SET NULL ON UPDATE SET
 * NULL', so should not pose data manipulation problems.
 *
 * @param toggleTriggers
 *
 * @return
 */

// DTRIG CF2012
@Override
public List<String> createExtras(boolean toggleTriggers) {
	final List<String> extras = new LinkedList<>();

	if (addFail) {
		// This hack is needed for MySQL to abort an insert if a trigger
		// fails.
		// This is disgusting, but is what MySQL documentation recommends
		// doing.
		extras.addAll(delimit("$$",
				"CREATE PROCEDURE constraint_failure(_message VARCHAR(255)) BEGIN" + lineSep
						+ "   -- This update is going to fail: this hack is needed because MySQL" + lineSep
						+ "   -- lacks the ability to do an (SQL-standard) SIGNAL from a procedure." + lineSep
						+ "   SET @sql = CONCAT('UPDATE `', _message, '` SET fail=1');" + lineSep
						+ "   PREPARE constraint_fail_statement_handle FROM @sql;" + lineSep
						+ "   EXECUTE contraint_fail_statement_handle;" + lineSep
						+ "   DEALLOCATE PREPARE contraint_fail_statement_handle;" + lineSep + "END"));
	}

	final List<StringBuilder> trigs = new LinkedList<>();

	for (final EntityNode table : triggers.keySet()) {
		final LinkedHashMap<String, LinkedList<String>> tableTriggers = triggers.get(table);

		for (final String when : tableTriggers.keySet()) {
			final LinkedList<String> actions = tableTriggers.get(when);
			final StringBuilder commands = new StringBuilder(200);

			commands.append("CREATE TRIGGER ")
					.append(quoteId(table + "_" + when.replaceAll("(\\w)\\w*\\s*", "$1").toLowerCase() + "Trig"))
					.append(' ').append(when).append(" ON ").append(quoteId(table)).append(" FOR EACH ROW")
					.append(lineSep);

			if (toggleTriggers) {
				commands.append("\tIF (@DISABLE_TRIGGER IS NULL) THEN ").append(lineSep);
			}

			if (actions.size() == 1) {
				commands.append(toggleTriggers ? "\t\t" : "\t").append(actions.getFirst()).append(";");
			} else {
				commands.append(toggleTriggers ? "\t\t" : "\t").append("BEGIN").append(lineSep);

				for (final String action : actions) {
					commands.append(toggleTriggers ? "\t\t\t" : "\t\t").append(action.replaceFirst(";\\s*$", ""))
							.append(';').append(lineSep);
				}

				commands.append(toggleTriggers ? "\t\t" : "\t").append("END;");
			}

			if (toggleTriggers) {
				commands.append(lineSep).append("\tEND IF;").append(lineSep);
			}

			trigs.add(commands);
		}
	}

	if (!trigs.isEmpty()) {
		extras.addAll(delimit("$$", trigs));
	}

	return extras;
}
 
Example 16
public static LinkedHashMap<AirMapRule.Status,List<AirMapRule>> getRulesWithFlightFeatures(AirMapRuleset ruleset, AirMapEvaluation evaluation) {
    LinkedHashMap<AirMapRule.Status,List<AirMapRule>> ruleStatusMap = new LinkedHashMap<>();
    // pre-populate status for correct order
    ruleStatusMap.put(AirMapRule.Status.Conflicting, new ArrayList<AirMapRule>());
    ruleStatusMap.put(AirMapRule.Status.MissingInfo, new ArrayList<AirMapRule>());
    ruleStatusMap.put(AirMapRule.Status.InformationRules, new ArrayList<AirMapRule>());
    ruleStatusMap.put(AirMapRule.Status.NotConflicting, new ArrayList<AirMapRule>());

    for (AirMapRule rule : ruleset.getRules()) {
        List<AirMapRule> rules = new ArrayList<>();
        if (ruleStatusMap.containsKey(rule.getStatus())) {
            rules = ruleStatusMap.get(rule.getStatus());
        }

        AirMapRule evaluationRule = getRuleFromEvaluation(evaluation, rule);
        for (AirMapFlightFeature flightFeature : CopyCollections.copy(rule.getFlightFeatures())) {
            Analytics.logDebug("ruleset", ruleset.getId());
            Analytics.logDebug("rule", rule.toString());
            AirMapFlightFeature evaluationFlightFeature = getFlightFeatureFromEvaluation(evaluationRule, flightFeature);
            if (evaluationFlightFeature == null) {
                rule.getFlightFeatures().remove(flightFeature);
                Timber.e("No match found for %s in evaluation", flightFeature.getFlightFeature());
                continue;
            }

            boolean ruleIsFailingDueToInput = rule.getStatus() != AirMapRule.Status.NotConflicting && !evaluationFlightFeature.isCalculated();
            boolean requiresInputBasedOnEvaluation = !evaluationFlightFeature.isCalculated() && evaluationRule.getStatus() != AirMapRule.Status.NotConflicting;

            // replace flight feature with the one from evaluation (includes the question)
            if (ruleIsFailingDueToInput || requiresInputBasedOnEvaluation) {
                rule.getFlightFeatures().remove(flightFeature);
                evaluationFlightFeature.setStatus(flightFeature.getStatus());
                rule.getFlightFeatures().add(evaluationFlightFeature);

            // otherwise hide flight feature
            } else {
                rule.getFlightFeatures().remove(flightFeature);
            }
        }

        rules.add(rule);
        ruleStatusMap.put(rule.getStatus(), rules);
    }

    // strip out empty sections
    for (AirMapRule.Status status : new HashSet<>(ruleStatusMap.keySet())) {
        if (ruleStatusMap.get(status).isEmpty()) {
            ruleStatusMap.remove(status);
        }
    }

    return ruleStatusMap;
}
 
Example 17
Source Project: gef   File: ContentBehavior.java    License: Eclipse Public License 2.0 4 votes vote down vote up
/**
 * Updates the host {@link IVisualPart}'s {@link IContentPart} children (see
 * {@link IVisualPart#getChildrenUnmodifiable()}) so that it is in sync with
 * the set of content children that is passed in.
 *
 * @param parent
 *            The parent {@link IVisualPart} whose content part children to
 *            synchronize against the given content children.
 *
 * @param contentChildren
 *            The list of content part children to be synchronized with the
 *            list of {@link IContentPart} children (
 *            {@link IContentPart#getChildrenUnmodifiable()}).
 *
 * @see IContentPart#getContentChildrenUnmodifiable()
 * @see IContentPart#getChildrenUnmodifiable()
 */
public void synchronizeContentPartChildren(
		IVisualPart<? extends Node> parent,
		final List<? extends Object> contentChildren) {
	if (contentChildren == null) {
		throw new IllegalArgumentException(
				"contentChildren may not be null");
	}

	List<IContentPart<? extends Node>> toRemove = new ArrayList<>();
	Map<IVisualPart<? extends Node>, List<IContentPart<? extends Node>>> removalsPerParent = new LinkedHashMap<>();
	detachAll(parent, Sets.newHashSet(contentChildren), toRemove,
			removalsPerParent);
	removalsPerParent.forEach((removeFrom, removeUs) -> {
		removeFrom.removeChildren(removeUs);
	});
	for (IContentPart<? extends Node> cp : toRemove) {
		disposeIfObsolete(cp);
	}

	LinkedHashMap<IVisualPart<? extends Node>, HashMultimap<Integer, IContentPart<? extends Node>>> addsPerParent = new LinkedHashMap<IVisualPart<? extends Node>, HashMultimap<Integer, IContentPart<? extends Node>>>();
	List<IContentPart<? extends Node>> added = Lists.newArrayList();
	List<ReorderData> reorders = Lists.newArrayList();
	addAll(parent, contentChildren, added, addsPerParent, reorders);

	ArrayList<IVisualPart<? extends Node>> parents = new ArrayList<IVisualPart<? extends Node>>(
			addsPerParent.keySet());

	for (int i = parents.size() - 1; i >= 0; i--) {
		IVisualPart<? extends Node> parentContentPart = parents.get(i);
		HashMultimap<Integer, IContentPart<? extends Node>> childContentParts = addsPerParent
				.get(parentContentPart);
		childContentParts.keySet().forEach(cp -> {
			ArrayList<IContentPart<? extends Node>> children = Lists
					.newArrayList(childContentParts.get(cp));
			parentContentPart.addChildren(children, cp);
			children.forEach(contentPart -> {
				synchronizeContentPartAnchorages(contentPart,
						contentPart.getContentAnchoragesUnmodifiable());
			});
		});
	}

	for (ReorderData rd : reorders) {
		rd.parent.reorderChild(rd.child, rd.index);
	}
}
 
Example 18
/**
 * e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
 * and pass in path to local location of file
 *
 * @param args
 */
public static void main(String[] args) throws Exception {

	int mb = 1024*1024;

	//Getting the runtime reference from system
	Runtime runtime = Runtime.getRuntime();

	System.out.println("##### Heap utilization statistics [MB] #####");

	//Print used memory
	System.out.println("Used Memory:"
			+ (runtime.totalMemory() - runtime.freeMemory()) / mb);

	//Print free memory
	System.out.println("Free Memory:"
			+ runtime.freeMemory() / mb);

	//Print total available memory
	System.out.println("Total Memory:" + runtime.totalMemory() / mb);

	//Print Maximum available memory
	System.out.println("Max Memory:" + runtime.maxMemory() / mb);


	if ( args.length < 1) {
		System.err.println("First argument needs to be path to fasta file");
		return;
	}

	File f = new File(args[0]);

	if ( ! f.exists()) {
		System.err.println("File does not exist " + args[0]);
		return;
	}

	long timeS = System.currentTimeMillis();

	// automatically uncompress files using InputStreamProvider
	InputStreamProvider isp = new InputStreamProvider();

	InputStream inStream = isp.getInputStream(f);


	FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
			inStream,
			new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
			new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));

	LinkedHashMap<String, ProteinSequence> b;

	int nrSeq = 0;

	while ((b = fastaReader.process(100)) != null) {
		for (String key : b.keySet()) {
			nrSeq++;
			System.out.println(nrSeq + " : " + key + " " + b.get(key));
			if ( nrSeq % 100000 == 0)
				System.out.println(nrSeq );
		}

	}
	long timeE = System.currentTimeMillis();
	System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
}
 
Example 19
private void paintTable(Graphics g) {

		if(kmf == null)
			return;
		KMFigureInfo kmfi = kmf.getKMFigureInfo();
		Graphics2D g2 = (Graphics2D) g;
		g2.setStroke(kmfi.kmStroke);
		SurvFitInfo sfi = kmf.getSurvivalFitInfo();

		LinkedHashMap<String, StrataInfo> sfiHashMap = new LinkedHashMap<String, StrataInfo>();
		if(sfi.isWeighted()){
			sfiHashMap = sfi.getUnweightedStrataInfoHashMap();
		}else{
			sfiHashMap = sfi.getStrataInfoHashMap();
		}

		if(sfiHashMap.size() == 0)
			return;
		//int height = this.getHeight();

		int row = 0;
		int left = kmf.getLeft();
		//int right = kmf.getRight();
		//int width = right - left;
		Font f = g2.getFont();
		Font nf = new Font(f.getName(), Font.BOLD, f.getSize());
		g2.setFont(nf);
		FontMetrics fm = getFontMetrics(nf);
		int index = 0;
		int fontHeight = getFontMetrics(getFont()).getHeight();
		int increment = fontHeight;
		ArrayList<Double> xaxisTimeValues = kmf.getxAxisTimeValues();
		ArrayList<Integer> xAxisTimeCoordinates = kmf.getxAxisTimeCoordinates();

		ArrayList<String> labels = new ArrayList<String>(sfiHashMap.keySet());
		Collections.sort(labels);

		for (String group : labels) {
			row = row + increment;
			g2.setColor(kmfi.getColor(index));
			index++;
			g2.drawLine(15, row - fontHeight/2, left - 5, row - fontHeight/2);
			g2.setColor(Color.BLACK);
			StrataInfo si = sfiHashMap.get(group);
			if(kmf.title.toString().equals("[APOBEC1 Transhera Observation Arm]")){
				//int dummy = 1;
			}
//           System.out.println(kmf.title + " Group " +  group);
//           System.out.println(si);
			for(int i = 0; i < xaxisTimeValues.size(); i++){
				Double time = xaxisTimeValues.get(i);
				int xvalue = xAxisTimeCoordinates.get(i);
				Double value = si.getNearestAtRisk(time);
				String nrisk = "";
				if(value == null){
					nrisk = "";
				}else{
					nrisk = String.valueOf(value.intValue());
				}
				if(time == 0.0){
					 g2.drawString(nrisk , xvalue, row);
				}else{
					int w = fm.stringWidth(nrisk );
					g2.drawString(nrisk , xvalue - w/2, row);
				}
			}

		}
	}
 
Example 20
@Override
public boolean execute(final CommandSender sender, String label, final String[] args){
	if(!this.plugin.isEnabled()) return false;
	if(!sender.hasPermission("economyapi.command.topmoney")){
		sender.sendMessage(TextFormat.RED + "You don't have permission to use this command.");
		return false;
	}
	
	try{
		final LinkedHashMap<String, Double> money = plugin.getAllMoney();
		final Set<String> players = money.keySet();
		final int page = args.length > 0 ? Math.max(1, Math.min(Integer.parseInt(args[0]), players.size())) : 1;
		new Thread(){
			public void run(){
				List<String> list = new LinkedList<>();
				for(String player:money.keySet()) list.add(player);
				
				Collections.sort(list, new Comparator<String>(){
					@Override
					public int compare(String s1, String s2) {
						double one = money.get(s1);
						double two = money.get(s2);
						return one < two ? 1 : one > two ? -1 : 0;
					}
				});
				
				StringBuilder output = new StringBuilder();
				output.append(plugin.getMessage("topmoney-tag", new String[]{Integer.toString(page), Integer.toString(((players.size() + 6) / 5))}, sender) + "\n");
				
				int duplicate = 0;
				double prev = -1D;
				for(int n = 0; n < list.size(); n++){
					double m = money.get(list.get(n));
					if(m == prev) duplicate++;
					else duplicate = 0;
					prev = m;
					int current = (int)Math.ceil((double)(n + 1) / 5);
					if(page == current){
						output.append(plugin.getMessage("topmoney-format", new String[]{Integer.toString(n + 1 - duplicate), list.get(n), Double.toString(m)}, sender) + "\n");
					}else if(page < current){
						break;
					}
				}
				output.substring(0, output.length() - 1);
				
				if(sender != null){
					sender.sendMessage(output.toString());
				}
			}
		}.start();
	}catch(NumberFormatException e){
		sender.sendMessage(TextFormat.RED + "Please provide a number.");
	}
	return true;
}