throw new Error(
"liftOver currently not implemented for transfer of annotation between different types of seqeunce");
}
- boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
- .getTo() == sq.getDatasetSequence()) : false;
+ boolean mapIsTo = (sp2sq != null)
+ ? (sp2sq.getTo() == sq
+ || sp2sq.getTo() == sq.getDatasetSequence())
+ : false;
// TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> mapForsq = new HashMap<>();
if (sequenceMapping != null)
{
if (sp2sq != null)
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
- /**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
- *
- * @param hiddenCols
- * @return
- */
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
public void setHiddenColumns(HiddenColumns cols);
+
+ /**
+ * Returns all HMM consensus sequences.
+ *
+ * @param remove
+ * If true, remove all HMM consensus sequences from the alignment.
+ * @return
+ */
+ public List<SequenceI> getHMMConsensusSequences(boolean remove);
+
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The idnex of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
+
+
}
*/
public List<DBRefEntry> getPrimaryDBRefs();
+ public void updateHMMMapping();
+
+ boolean isHMMConsensusSequence();
+
+ void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+ boolean hasHMMAnnotation();
+
+ void setHasInfo(boolean status);
+
+ int getPreviousPosition();
+
+ void setPreviousPosition(int previousPosition);
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * returns true.
+ */
+ BitSet getInsertionsAsBits();
}
ViewportRanges vpRanges;
public AlignViewControllerI avc;
-
+ /*
+ * The selected HMM for this align frame
+ */
+ HiddenMarkovModel selectedHMM = null;
List<AlignmentPanel> alignPanels = new ArrayList<>();
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
- .getSelectionGroup().getEndRes();
- for (int[] region : viewport.getAlignment().getHiddenColumns()
- .getHiddenRegions())
++
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+ ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy();
+ for (int[] region : hiddenRegions)
++
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
+ initInformation();
+
- String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
++
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
if (schemeName == null)
}
else if (label.indexOf("Consensus") > -1)
{
+
+
pop.addSeparator();
// av and sequencegroup need to implement same interface for
- final AlignmentAnnotation aaa = aa[selectedRow];
+
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
-
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
@Override
.setContents(new StringSelection(output), Desktop.instance);
ArrayList<int[]> hiddenColumns = null;
+
if (av.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<>();
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getHiddenRegions())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
++
+ hiddenColumns = av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
++
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
* currently selected sequence (if there is one):
*/
final List<SequenceI> selectedSequence = (seq == null
- ? Collections.<SequenceI> emptyList()
- : Arrays.asList(seq));
+ ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
++
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
+ showGroupConsensus
+ .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ showGroupConservation.setSelected(
+ Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo
+ .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
- showNpTooltip.setSelected(Cache
- .getDefault("SHOW_NPFEATS_TOOLTIP", true));
- showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
- true));
+ showNpTooltip
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
--- /dev/null
+package jalview.io;
+
++import jalview.api.AlignExportSettingI;
++import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+
+/**
+ * Adds capability to read in and write out HMMER3 files. .
+ *
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMFile extends AlignFile
+ implements AlignmentFileReaderI, AlignmentFileWriterI
+{
+ // HMM to store file data
+ private HiddenMarkovModel hmm;
+
+ // number of possible transitions
+ private static final int NUMBER_OF_TRANSITIONS = 7;
+
- private static final String NL = "\n";
++ private String NL = "\n";
+
+ //number of symbols in the alphabet used in the hidden Markov model
+ int numberOfSymbols;
+
+ private final String SPACE = " ";
+
+ private final String COMPO = "COMPO";
+
+ private final String EMPTY = "";
+
+ //This is a line that needs to be added to each HMMER� file. It is purely for readability.
+ private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
+
+ /**
+ * Parses immediately.
+ *
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public HMMFile(String inFile, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * Parses immediately.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public HMMFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Default constructor, do not use!
+ */
+ public HMMFile()
+ {
+
+ }
+
+ /**
+ * Constructor for HMMFile used for exporting.
+ *
+ * @param hmm
+ * @param exportImmediately
+ */
+ public HMMFile(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+
+ /**
+ * For testing, do not use.
+ *
+ * @param br
+ */
+ HMMFile(BufferedReader br)
+ {
+ dataIn = br;
+ }
+
+ /**
+ * Returns the HMM produced by reading in a HMMER3 file.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ /**
+ * Sets the HMM used in this file.
+ *
+ * @param model
+ */
+ public void setHMM(HiddenMarkovModel model)
+ {
+ this.hmm = model;
+ }
+
+ /**
+ * Gets the name of the hidden Markov model.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return hmm.getName();
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM field on this object.
+ *
+ * @throws IOException
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ hmm = new HiddenMarkovModel();
+ parseFileProperties(dataIn);
+ parseModel(dataIn);
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM field on this object.
+ *
+ * @throws IOException
+ */
+
+ public void parse(BufferedReader br) throws IOException
+ {
+ hmm = new HiddenMarkovModel();
+ parseFileProperties(br);
+ parseModel(br);
+ }
+
+
+
+ /**
+ * Imports the file properties from a HMMER3 file.
+ *
+ * @param input
+ * The buffered reader used to read in the file.
+ * @throws IOException
+ */
+ void parseFileProperties(BufferedReader input) throws IOException
+ {
+ boolean readingFile = true;
+ hmm.setFileHeader(input.readLine());
+ String line = input.readLine();
+ while (readingFile)
+ {
+ if (line != null)
+ {
+ Scanner parser = new Scanner(line);
+ String next = parser.next();
+ if ("HMM".equals(next)) // indicates start of HMM data (end of file
+ // properties)
+ {
+ readingFile = false;
+ fillSymbols(parser);
+ numberOfSymbols = hmm.getNumberOfSymbols();
+ }
+ else if ("STATS".equals(next))
+ {
+ parser.next();
+ String key;
+ String value;
+ key = parser.next();
+ value = parser.next() + SPACE + SPACE + parser.next();
+ hmm.addFileProperty(key, value);
+ }
+ else
+ {
+ String key = next;
+ String value = parser.next();
+ while (parser.hasNext())
+ {
+ value = value + SPACE + parser.next();
+ }
+ hmm.addFileProperty(key, value);
+ }
+ parser.close();
+ }
+ line = input.readLine();
+ if (line == null)
+ {
+ readingFile = false;
+ }
+ }
+
+ }
+
+ /**
+ * Parses the model data from the HMMER3 file
+ *
+ * @param input
+ * The buffered reader used to read the file.
+ * @throws IOException
+ */
+ void parseModel(BufferedReader input) throws IOException
+ {
+ String line = input.readLine();
+ int node = 0;
+ while (!"//".equals(line))
+ {
+ hmm.getNodes().add(new HMMNode());
+ String next;
+ Scanner matchReader = new Scanner(line);
+ next = matchReader.next();
+ if (next.equals(COMPO) || node > 0)
+ {
+ // stores match emission line in list
+ List<Double> matches = new ArrayList<>();
+ matches = fillList(matchReader, numberOfSymbols);
+ hmm.getNodes().get(node).setMatchEmissions(matches);
+ if (node > 0)
+ {
+ parseAnnotations(matchReader, node);
+ }
+ }
+ matchReader.close();
+ // stores insert emission line in list
+ line = input.readLine();
+ Scanner insertReader = new Scanner(line);
+ List<Double> inserts = new ArrayList<>();
+ inserts = fillList(insertReader, numberOfSymbols);
+ hmm.getNodes().get(node).setInsertEmissions(inserts);
+ insertReader.close();
+
+ // stores state transition line in list
+ line = input.readLine();
+ Scanner transitionReader = new Scanner(line);
+ List<Double> transitions = new ArrayList<>();
+ transitions = fillList(transitionReader, NUMBER_OF_TRANSITIONS);
+ hmm.getNodes().get(node).setStateTransitions(transitions);
+ transitionReader.close();
+ line = input.readLine();
+ node++;
+ }
+
+ }
+
+ /**
+ * Parses the annotations on the match emission line.
+ *
+ * @param scanner
+ * The scanner which is processing match emission line.
+ * @param index
+ * The index of node which is being scanned.
+ */
+ void parseAnnotations(Scanner scanner, int index)
+ {
+ if (hmm.mapIsActive() && scanner.hasNext())
+ {
+ int column;
+ column = scanner.nextInt();
+ hmm.getNodes().get(index).setAlignmentColumn(column - 1);
+ hmm.getNodeLookup().put(column - 1, index);
+ }
+ else
+ {
+ scanner.next();
+ }
+
+ if (scanner.hasNext())
+ {
+ char consensusR;
+ consensusR = charValue(scanner.next());
+ hmm.getNodes().get(index).setConsensusResidue(consensusR);
+ }
+
+ if (scanner.hasNext())
+ {
+ char reference;
+ reference = charValue(scanner.next());
+ hmm.getNodes().get(index).setReferenceAnnotation(reference);
+ }
+
+ if (scanner.hasNext())
+ {
+ char value;
+ value = charValue(scanner.next());
+ hmm.getNodes().get(index).setMaskValue(value);
+ }
+ if (scanner.hasNext())
+ {
+ char consensusS;
+ consensusS = charValue(scanner.next());
+ hmm.getNodes().get(index).setConsensusStructure(consensusS);
+ }
+ }
+
+
+
+ /**
+ * Fills a list of doubles based on an input line.
+ *
+ * @param input
+ * The scanner for the line containing the data to be transferred to
+ * the list.
+ * @param numberOfElements
+ * The number of elements in the list to be filled.
+ * @return filled list Returns the list of doubles.
+ * @throws IOException
+ */
+ static List<Double> fillList(Scanner input,
+ int numberOfElements) throws IOException
+ {
+ List<Double> list = new ArrayList<>();
+ for (int i = 0; i < numberOfElements; i++)
+ {
+
+ String next = input.next();
+ if (next.contains("*")) // state transitions to or from delete states
+ // occasionally have values of -infinity. These
+ // values are represented by an * in the .hmm
+ // file.
+ {
+ list.add(Double.NEGATIVE_INFINITY);
+ }
+ else
+ {
+ double prob = Double.valueOf(next);
+ prob = Math.pow(Math.E, -prob);
+ list.add(prob);
+ }
+ }
+ if (list.size() < numberOfElements)
+ {
+ throw new IOException("Incomplete data");
+ }
+ return list;
+ }
+
+ /**
+ * Returns a string to be added to the StringBuilder containing the entire
+ * output String.
+ *
+ * @param initialColumnSeparation
+ * The initial whitespace separation between the left side of the
+ * file and first character.
+ * @param columnSeparation
+ * The separation between subsequent data entries.
+ * @param data
+ * The list fo data to be added to the String.
+ * @return
+ */
+ String addData(int initialColumnSeparation,
+ int columnSeparation, List<String> data)
+ {
+ String line = EMPTY;
+ int index = 0;
+ for (String value : data)
+ {
+ if (index == 0)
+ {
+ line += String.format("%" + initialColumnSeparation + "s", value);
+ }
+ else
+ {
+ line += String.format("%" + columnSeparation + "s", value);
+ }
+ index++;
+ }
+ return line;
+ }
+
+ /**
+ * Converts list of characters into a list of Strings.
+ *
+ * @param list
+ * @return Returns the list of Strings.
+ */
+ List<String> charListToStringList(List<Character> list)
+ {
+ List<String> strList = new ArrayList<>();
+ for (char value : list)
+ {
+ String strValue = Character.toString(value);
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Converts a list of doubles into a list of Strings, rounded to the nearest
+ * 5th decimal place.
+ *
+ * @param list
+ * @param noOfDecimals
+ * @return
+ */
+ List<String> doubleListToStringList(List<Double> list)
+ {
+ List<String> strList = new ArrayList<>();
+ for (double value : list)
+ {
+ String strValue;
+ if (value > 0)
+ {
+ strValue = String.format("%.5f", value);
+
+ }
+ else if (value == -0.00000d)
+ {
+ strValue = "0.00000";
+ }
+ else
+ {
+ strValue = "*";
+ }
+
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Converts a primitive array of Strings to a list of Strings.
+ *
+ * @param array
+ * @return
+ */
+ List<String> stringArrayToStringList(String[] array)
+ {
+ List<String> list = new ArrayList<>();
+ for (String value : array)
+ {
+ list.add(value);
+ }
+
+ return list;
+ }
+
+ /**
+ * Returns a string containing the model data.
+ */
+ String getModelAsString()
+ {
+ StringBuffer output = new StringBuffer();
+ String symbolLine = "HMM";
+ List<Character> charSymbols = hmm.getSymbols();
+ List<String> strSymbols;
+ strSymbols = charListToStringList(charSymbols);
+ symbolLine += addData(11, 9, strSymbols);
+ output.append(symbolLine);
+ output.append(NL + TRANSITIONTYPELINE);
+
+ int length = hmm.getLength();
+
+ for (int node = 0; node <= length; node++)
+ {
+ String matchLine;
+ if (node == 0)
+ {
+ matchLine = String.format("%7s", "COMPO");
+ }
+ else
+ {
+ matchLine = String.format("%7s", node);
+ }
+
+ List<String> strMatches;
+ List<Double> doubleMatches;
+ doubleMatches = convertListToLogSpace(
+ hmm.getNode(node).getMatchEmissions());
+ strMatches = doubleListToStringList(doubleMatches);
+ matchLine += addData(10, 9, strMatches);
+
+
+ if (node != 0)
+ {
+ matchLine += SPACE + (hmm.getNodeAlignmentColumn(node) + 1);
+ matchLine += SPACE + hmm.getConsensusResidue(node);
+ matchLine += SPACE + hmm.getReferenceAnnotation(node);
+ if (hmm.getFileHeader().contains("HMMER3/f"))
+ {
+ matchLine += SPACE + hmm.getMaskedValue(node);
+ matchLine += SPACE + hmm.getConsensusStructure(node);
+ }
+
+ }
+
+ output.append(NL + matchLine);
+
+ String insertLine = EMPTY;
+ List<String> strInserts;
+ List<Double> doubleInserts;
+ doubleInserts = convertListToLogSpace(
+ hmm.getNode(node).getInsertEmissions());
+ strInserts = doubleListToStringList(doubleInserts);
+ insertLine += addData(17, 9, strInserts);
+
+ output.append(NL + insertLine);
+
+ String transitionLine = EMPTY;
+ List<String> strTransitions;
+ List<Double> doubleTransitions;
+ doubleTransitions = convertListToLogSpace(
+ hmm.getNode(node).getStateTransitions());
+ strTransitions = doubleListToStringList(doubleTransitions);
+ transitionLine += addData(17, 9, strTransitions);
+
+ output.append(NL + transitionLine);
+ }
+ return output.toString();
+ }
+
+ /**
+ * Returns a String containing the HMM file properties
+ */
+ String getFilePropertiesAsString()
+ {
+ StringBuffer output = new StringBuffer();
+ String line;
+
+ output.append(hmm.getFileHeader());
+
+ line = String.format("%-5s %1s", "NAME", hmm.getName());
+ output.append(NL + line);
+
+ if (hmm.getAccessionNumber() != null)
+ {
+ line = String.format("%-5s %1s", "ACC", hmm.getAccessionNumber());
+ output.append(NL + line);
+ }
+
+ if (hmm.getDescription() != null)
+ {
+ line = String.format("%-5s %1s", "DESC", hmm.getDescription());
+ output.append(NL + line);
+ }
+ line = String.format("%-5s %1s", "LENG", hmm.getLength());
+ output.append(NL + line);
+
+ if (hmm.getMaxInstanceLength() != null)
+ {
+ line = String.format("%-5s %1s", "MAXL", hmm.getMaxInstanceLength());
+ output.append(NL + line);
+ }
+ line = String.format("%-5s %1s", "ALPH", hmm.getAlphabetType());
+ output.append(NL + line);
+
+ boolean status;
+ String statusStr;
+
+ status = hmm.referenceAnnotationIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "RF",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.maskValueIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "MM",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.consensusResidueIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "CONS",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.consensusStructureIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "CS",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.mapIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "MAP",
+ statusStr);
+ output.append(NL + line);
+
+
+ if (hmm.getDate() != null)
+ {
+ line = String.format("%-5s %1s", "DATE", hmm.getDate());
+ output.append(NL + line);
+ }
+ if (hmm.getNumberOfSequences() != null)
+ {
+ line = String.format("%-5s %1s", "NSEQ", hmm.getNumberOfSequences());
+ output.append(NL + line);
+ }
+ if (hmm.getEffectiveNumberOfSequences() != null)
+ {
+ line = String.format("%-5s %1s", "EFFN",
+ hmm.getEffectiveNumberOfSequences());
+ output.append(NL + line);
+ }
+ if (hmm.getCheckSum() != null)
+ {
+ line = String.format("%-5s %1s", "CKSUM", hmm.getCheckSum());
+ output.append(NL + line);
+ }
+ if (hmm.getGatheringThreshold() != null)
+ {
+ line = String.format("%-5s %1s", "GA", hmm.getGatheringThreshold());
+ output.append(NL + line);
+ }
+
+ if (hmm.getTrustedCutoff() != null)
+ {
+ line = String.format("%-5s %1s", "TC", hmm.getTrustedCutoff());
+ output.append(NL + line);
+ }
+ if (hmm.getNoiseCutoff() != null)
+ {
+ line = String.format("%-5s %1s", "NC", hmm.getNoiseCutoff());
+ output.append(NL + line);
+ }
+ if (hmm.getMSV() != null)
+ {
+ line = String.format("%-19s %18s", "STATS LOCAL MSV", hmm.getMSV());
+ output.append(NL + line);
+
+ line = String.format("%-19s %18s", "STATS LOCAL VITERBI",
+ hmm.getViterbi());
+ output.append(NL + line);
+
+ line = String.format("%-19s %18s", "STATS LOCAL FORWARD",
+ hmm.getForward());
+ output.append(NL + line);
+ }
+ return output.toString();
+ }
+
+
+ /**
+ * Returns the char value of a single lettered String.
+ *
+ * @param string
+ * @return
+ */
+ char charValue(String string)
+ {
+ char character;
+ character = string.charAt(0);
+ return character;
+
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
++ if (seqs[0].getHMM() != null)
++ {
++ hmm = seqs[0].getHMM();
++ }
+ return print();
+ }
+
+ /**
+ * Prints the .hmm file to a String.
+ *
+ * @return
+ */
+ public String print()
+ {
+ StringBuffer output = new StringBuffer();
+ output.append(getFilePropertiesAsString());
+ output.append(NL);
+ output.append(getModelAsString());
+ output.append(NL + "//");
+ return output.toString();
+ }
+
+ /**
+ * Converts the probabilities contained in a list into log space.
+ *
+ * @param list
+ */
+ List<Double> convertListToLogSpace(List<Double> list)
+ {
+
+ List<Double> convertedList = new ArrayList<>();
+ for (int i = 0; i < list.size(); i++)
+ {
+ double prob = list.get(i);
+ double logProb = -1 * Math.log(prob);
+
+ convertedList.add(logProb);
+ }
+ return convertedList;
+
+
+ }
+
+ /**
+ * Returns the HMM sequence produced by reading a .hmm file.
+ */
+ @Override
+ public SequenceI[] getSeqsAsArray()
+ {
+ SequenceI hmmSeq = hmm.initHMMSequence();
+ SequenceI[] seq = new SequenceI[1];
+ seq[0] = hmmSeq;
+ return seq;
+
+ }
+
+ /**
+ * Fills symbol array and adds each symbol to an index lookup
+ *
+ * @param parser
+ * The scanner scanning the symbol line in the file.
+ */
+ public void fillSymbols(Scanner parser)
+ {
+ int i = 0;
+ while (parser.hasNext())
+ {
+ String strSymbol = parser.next();
+ char[] symbol = strSymbol.toCharArray();
+ hmm.getSymbols().add(symbol[0]);
+ hmm.setSymbolIndex(symbol[0], i);
+ i++;
+ }
+ }
+
++ @Override
++ public void setNewlineString(String newLine)
++ {
++ NL = newLine;
++ }
++
++ @Override
++ public void setExportSettings(AlignExportSettingI exportSettings)
++ {
++
++ }
++
++ @Override
++ public void configureForView(AlignmentViewPanel viewpanel)
++ {
++
++ }
++
++ @Override
++ public boolean hasWarningMessage()
++ {
++ return false;
++ }
++
++ @Override
++ public String getWarningMessage()
++ {
++ return "warning message";
++ }
++
+}
+
}
}
+
- // output annotations
- while (i < s.length && s[i] != null)
- {
- AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+ // output annotations
+ while (i < s.length && s[i] != null)
+ {
+ AlignmentAnnotation[] alAnot = s[i].getAnnotation();
if (alAnot != null)
+ {
+ Annotation[] ann;
+ for (int j = 0; j < alAnot.length; j++)
{
- Annotation[] ann;
- for (int j = 0; j < alAnot.length; j++)
- {
- String key = type2id(alAnot[j].label);
- boolean isrna = alAnot[j].isValidStruc();
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
-
+ if (isrna)
+ {
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
+ }
+ if (key == null)
+ {
- if (isrna)
- {
- // hardwire to secondary structure if there is RNA secondary
- // structure on the annotation
- key = "SS";
- }
- if (key == null)
- {
+ continue;
+ }
- continue;
- }
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+ ann = alAnot[j].annotations;
+ String seq = "";
+ for (int k = 0; k < ann.length; k++)
+ {
+ seq += outputCharacter(key, k, isrna, ann, s[i]);
- }
+
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form(
- "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
- ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
- {
- seq += outputCharacter(key, k, isrna, ann, s[i]);
- }
- out.append(seq);
- out.append(newline);
- }
+ }
-
- out.append(new Format("%-" + maxid + "s")
- .form(printId(s[i], jvSuffix) + " "));
- out.append(s[i].getSequenceAsString());
- out.append(newline);
- i++;
+ out.append(seq);
+ out.append(newline);
+ }
}
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[i], jvSuffix) + " "));
+ out.append(s[i].getSequenceAsString());
+ out.append(newline);
+ i++;
+ }
+
// alignment annotation
AlignmentAnnotation aa;
if (al.getAlignmentAnnotation() != null)
out.append(newline);
}
}
++
+
out.append("//");
out.append(newline);
out.append("# STOCKHOLM 1.0");
out.append(newline);
print(getSeqsAsArray(), false);
--
++
+ out.append("//");
out.append(newline);
return out.toString();
}
saveAs_actionPerformed(e);
}
};
-
+
// FIXME getDefaultToolkit throws an exception in Headless mode
- KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+
closeMenuItem.setText(MessageManager.getString("action.close"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+ String status = Cache.getProperty("HMMER_FUNCTIONING");
+ if ("false".equals(status) || status == null)
+ {
+ hmmerMenu.setEnabled(false);
+ }
+ else
+ {
+ hmmerMenu.setEnabled(true);
+ }
+ hmmerMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmerMenu_actionPerformed(e);
+ }
+ });
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
sortGroupMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager
- .getString("label.out_to_textbox"));
-
++
+ outputTextboxMenu
+ .setText(MessageManager.getString("label.out_to_textbox"));
+
++
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
- true));
+ annotationPanelMenuItem
+ .setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem
+ .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
MessageManager.getString("label.sort_annotations_by_sequence"));
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
-
- sortAnnBySequence
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+
++
+ sortAnnBySequence.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
{
@Override
overviewMenuItem_actionPerformed(e);
}
});
-
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
wrapMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
renderGapsMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
}
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
-
- showSeqFeatures.setText(MessageManager
- .getString("label.show_sequence_features"));
+
+ showSeqFeatures.setText(
+ MessageManager.getString("label.show_sequence_features"));
++
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager
- .getString("label.show_database_refs"));
+ showDbRefsMenuitem
+ .setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
- showNpFeatsMenuitem.setText(MessageManager
- .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(
+ MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
- showGroupConservation.setText(MessageManager
- .getString("label.group_conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
-
- showGroupConsensus.setText(MessageManager
- .getString("label.group_consensus"));
+
+ showGroupConsensus
+ .setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
- showConsensusHistogram.setText(MessageManager
- .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(
+ MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
});
- showSequenceLogo.setText(MessageManager
- .getString("label.show_consensus_logo"));
+ showSequenceLogo
+ .setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
-
+
});
- normaliseSequenceLogo.setText(MessageManager
- .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo
+ .setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
- applyAutoAnnotationSettings.setText(MessageManager
- .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings
+ .setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
sortAnnotations_actionPerformed();
}
});
-
+
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
annotationColumn_actionPerformed(e);
}
});
-
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+
copy.setText(MessageManager.getString("action.copy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
-
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
-
+
cut.setText(MessageManager.getString("action.cut"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager
- .getString("label.save_png_image"));
-
+ createPNG.setActionCommand(
+ MessageManager.getString("label.save_png_image"));
-
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
createSVG(null);
}
});
-
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
- loadTreeMenuItem.setActionCommand(MessageManager
- .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.setActionCommand(
+ MessageManager.getString("label.load_tree_for_sequence_set"));
loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager
- .getString("label.automatic_scrolling"));
+ followHighlightMenuItem
+ .setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
});
extractScores.setVisible(true);
// JBPNote: TODO: make gui for regex based score extraction
-
+
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+
runGroovy.setText(MessageManager.getString("label.run_groovy"));
- runGroovy.setToolTipText(MessageManager
- .getString("label.run_groovy_tip"));
+ runGroovy.setToolTipText(
+ MessageManager.getString("label.run_groovy_tip"));
runGroovy.addActionListener(new ActionListener()
{
@Override
@Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ try
+ {
+ associatedData_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
- autoCalculate.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculate.setState(jalview.bin.Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
hiddenMarkers_actionPerformed(e);
}
});
-
+
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK,
+ false);
al = new ActionListener()
{
@Override
tabbedPane_focusGained(e);
}
});
-
+
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
reload_actionPerformed(e);
}
});
-
+
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
-
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
-
- idRightAlign.setText(MessageManager
- .getString("label.right_align_sequence_id"));
+
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
@Override
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
* Customer cell editor for JTable: supports column of radio buttons in
* conjunction with renderer
*/
- public class RadioButtonEditor extends AbstractCellEditor implements
- TableCellEditor
- {
- private JRadioButton button = new JRadioButton();
+ public class RadioButtonEditor extends AbstractCellEditor
+ implements TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
- public RadioButtonEditor()
- {
+ public RadioButtonEditor()
+ {
button.setHorizontalAlignment(SwingConstants.CENTER);
this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fireEditingStopped();
- }
- });
- }
+ fireEditingStopped();
+ }
+ });
+ }
- @Override
- public Component getTableCellEditorComponent(JTable table,
- Object value, boolean isSelected, int row, int column)
- {
+ @Override
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
button.setSelected((boolean) value);
- return button;
- }
+ return button;
+ }
- @Override
- public Object getCellEditorValue()
- {
+ @Override
+ public Object getCellEditorValue()
+ {
return button.isSelected();
- }
+ }
}
+
+ public void hmmerPath_actionPerformed(ActionEvent e)
+ {
+
+ }
}
* the order of declaration is the default order in which
* items are added to Colour menus
*/
- Clustal("Clustal", ClustalxColourScheme.class), Blosum62("Blosum62",
- Blosum62ColourScheme.class), PID("% Identity",
- PIDColourScheme.class), Zappo("Zappo", ZappoColourScheme.class),
- Taylor("Taylor", TaylorColourScheme.class), Hydrophobic("Hydrophobic",
- HydrophobicColourScheme.class), Helix("Helix Propensity",
- HelixColourScheme.class), Strand("Strand Propensity",
- StrandColourScheme.class), Turn("Turn Propensity",
- TurnColourScheme.class), Buried("Buried Index",
- BuriedColourScheme.class), Nucleotide("Nucleotide",
- NucleotideColourScheme.class), PurinePyrimidine(
- "Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
- RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee(
- "T-Coffee Scores", TCoffeeColourScheme.class),
+ Clustal("Clustal", ClustalxColourScheme.class),
+ Blosum62("Blosum62", Blosum62ColourScheme.class),
+ PID("% Identity", PIDColourScheme.class),
+ Zappo("Zappo", ZappoColourScheme.class),
+ Taylor("Taylor", TaylorColourScheme.class),
+ Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
+ Helix("Helix Propensity", HelixColourScheme.class),
+ Strand("Strand Propensity", StrandColourScheme.class),
+ Turn("Turn Propensity", TurnColourScheme.class),
+ Buried("Buried Index", BuriedColourScheme.class),
+ Nucleotide("Nucleotide", NucleotideColourScheme.class),
+ PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
+ RNAHelices("RNA Helices", RNAHelicesColour.class),
- TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
++ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+ HMMER("HMMER", HMMERColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
{
restartable = Collections
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
- blackList = Collections
- .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
+ blackList = Collections.synchronizedList(
+ new ArrayList<Class<? extends AlignCalcWorkerI>>());
inProgress = Collections
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
- updating = Collections
- .synchronizedMap(new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
+ updating = Collections.synchronizedMap(
+ new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
- canUpdate = new HashSet<AlignCalcWorkerI>();
+ canUpdate = new HashSet<>();
}
@Override
git://source.jalview.org / jalview.git / commitdiff