X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=009d94610ba2e732752085fcfaf1314fa26409f7;hb=04a4d60a50394d846d0479c442facebe360b5b9c;hp=4c9360ed739f233c266dd6850566c46e902b2ae8;hpb=653e250e0a2a5dd455ae4c52794c4ce0de340418;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4c9360e..009d946 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -54,6 +54,7 @@ import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; @@ -62,6 +63,12 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMAlign; +import jalview.hmmer.HMMBuild; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearch; +import jalview.hmmer.HmmerCommand; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -88,6 +95,7 @@ import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; +import jalview.util.StringUtils; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; @@ -95,6 +103,10 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.ParamDatastoreI; +import jalview.ws.params.WsParamSetI; +import jalview.ws.params.simple.Option; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; @@ -124,22 +136,29 @@ import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; +import java.io.IOException; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.Deque; import java.util.Enumeration; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; +import java.util.Map; +import java.util.Scanner; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; +import javax.swing.JFileChooser; +import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; +import javax.swing.JOptionPane; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -153,6 +172,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { + Map distribution = new HashMap<>(); // temporary + public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -165,6 +186,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; public AlignViewControllerI avc; + /* + * The selected HMM for this align frame + */ + SequenceI selectedHMMSequence; List alignPanels = new ArrayList<>(); @@ -178,6 +203,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + /** * Creates a new AlignFrame object with specific width and height. * @@ -762,6 +788,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); } } @@ -904,6 +931,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + showInformationHistogram.setSelected(av.isShowInformationHistogram()); + showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo()); + normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); @@ -995,6 +1025,198 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void hmmBuild_actionPerformed(boolean withDefaults) + { + if (!alignmentIsSufficient(1)) + { + return; + } + List args = new ArrayList<>(); + if (withDefaults) + { + // todo: construct this in HMMERPreset? + String argName = MessageManager.getString("label.hmmbuild_for"); + String argValue = MessageManager.getString("label.alignment"); + args.add( + new Option(argName, null, false, null, argValue, null, null)); + } + else + { + WsParamSetI set = new HMMERPreset(); + ParamDatastoreI store = HMMERParamStore.forBuild(); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMBuild(this, args)).start(); + } + + @Override + public void hmmAlign_actionPerformed(boolean withDefaults) + { + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + List args = new ArrayList<>(); + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + ParamDatastoreI store = HMMERParamStore.forAlign(); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMAlign(this, args)).start(); + } + + @Override + public void hmmSearch_actionPerformed(boolean withDefaults) + { + if (!checkForHMM()) + { + return; + } + List args = new ArrayList<>(); + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + ParamDatastoreI store = HMMERParamStore.forSearch(); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); + } + + /** + * Checks if the frame has a selected hidden Markov model + * + * @return + */ + private boolean checkForHMM() + { + if (getSelectedHMM() == null) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.no_selected_hmm")); + return false; + } + return true; + } + + /** + * Checks if the alignment contains the required number of sequences. + * + * @param required + * @return + */ + public boolean alignmentIsSufficient(int required) + { + if (getViewport().getAlignment().getSequences().size() < required) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.not_enough_sequences")); + return false; + } + return true; + } + + @Override + public void addDatabase_actionPerformed() throws IOException + { + if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null) + { + Cache.setProperty(Preferences.HMMSEARCH_DBS, ""); + Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, ""); + } + + String path = openFileChooser(false); + if (new File(path).exists()) + { + IdentifyFile identifier = new IdentifyFile(); + FileFormatI format = identifier.identify(path, DataSourceType.FILE); + if (format == FileFormat.Fasta || format == FileFormat.Stockholm + || format == FileFormat.Pfam) + { + String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS); + String currentDbPaths = Cache + .getProperty(Preferences.HMMSEARCH_DB_PATHS); + currentDbPaths += " " + path; + + String fileName = StringUtils.getLastToken(path, File.separator); + Scanner scanner = new Scanner(fileName).useDelimiter("."); + String name = scanner.next(); + scanner.close(); + currentDbs += " " + path; // TODO remove path from file name + scanner.close(); + + Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths); + Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths); + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.not_enough_sequences")); + } + } + + /** + * Opens a file chooser + * + * @param forFolder + * @return + */ + protected String openFileChooser(boolean forFolder) + { + String choice = null; + JFileChooser chooser = new JFileChooser(); + if (forFolder) + { + chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + } + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); + + int value = chooser.showOpenDialog(this); + + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; + } + + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) @@ -1403,6 +1625,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( @@ -1828,7 +2051,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1864,23 +2086,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - ArrayList hiddenRegions = viewport.getAlignment() - .getHiddenColumns().getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns - .add(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); - } - } + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, @@ -1895,9 +2111,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(true); } @@ -1907,9 +2126,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(false); } @@ -1919,8 +2141,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param newAlignment * true to paste to a new alignment, otherwise add to this. + * @throws InterruptedException + * @throws IOException */ - void paste(boolean newAlignment) + void paste(boolean newAlignment) throws IOException, InterruptedException { boolean externalPaste = true; try @@ -2209,11 +2433,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -2251,7 +2472,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2268,11 +2488,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -4554,6 +4771,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * either a filename or a URL string. + * @throws InterruptedException + * @throws IOException */ public void loadJalviewDataFile(String file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) @@ -4641,11 +4860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@ -4664,7 +4879,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); @@ -4867,14 +5081,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); @@ -5588,6 +5803,68 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** + * Sets the status of the HMMER menu + */ + public void updateHMMERStatus() + { + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + } + + /** + * Returns the selected hidden Markov model. + * + * @return + */ + public HiddenMarkovModel getSelectedHMM() + { + if (selectedHMMSequence == null) + { + return null; + } + return selectedHMMSequence.getHMM(); + } + + /** + * Returns the selected hidden Markov model. + * + * @return + */ + public SequenceI getSelectedHMMSequence() + { + return selectedHMMSequence; + } + + /** + * Sets the selected hidden Markov model + * + * @param selectedHMM + */ + public void setSelectedHMMSequence(SequenceI selectedHMM) + { + this.selectedHMMSequence = selectedHMM; + hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to " + + selectedHMM.getHMM().getName()); + hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with " + + selectedHMM.getHMM().getName()); + } + + @Override + public void hmmerMenu_actionPerformed(ActionEvent e) + { + SequenceGroup grp = getViewport().getSelectionGroup(); + if (grp != null) + { + hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from " + + grp.getName()); + } + else + { + hmmBuild.setText(MessageManager.getString("label.hmmbuild") + + " from Alignment"); + } + } + @Override protected void loadVcf_actionPerformed() {