X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=d30f10dfa5ca249bdf946b10bdbe9dd85a24b776;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=8f1f2fd8d9b2e3c4fb65f47d3787a91040b3e7b5;hpb=bf0d052fef43e9809b7170dbfd372b3ea116391b;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 8f1f2fd..d30f10d 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -49,7 +49,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -60,7 +64,7 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -102,7 +106,6 @@ import java.net.URLEncoder; import java.util.Arrays; import java.util.Deque; import java.util.HashMap; -import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.StringTokenizer; @@ -219,6 +222,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setColumnSelection(columnSelection); } + viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel = new AlignmentPanel(this, viewport); avc = new jalview.controller.AlignViewController(this, viewport, @@ -294,6 +298,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { RNAHelixColour.setEnabled(false); purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for @@ -345,7 +350,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * is protocol for accessing data referred to by file */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType type) { return parseFeaturesFile(file, type, true); } @@ -355,14 +360,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * * @param file * file URL, content, or other resolvable path - * @param type + * @param sourceType * is protocol for accessing data referred to by file * @param autoenabledisplay * when true, display features flag will be automatically enabled if * features are loaded * @return true if data parsed as a features file */ - public boolean parseFeaturesFile(String file, String type, + public boolean parseFeaturesFile(String file, DataSourceType sourceType, boolean autoenabledisplay) { boolean featuresFile = false; @@ -372,7 +377,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getFeatureRenderer().getFeatureColours(); boolean relaxedIdMatching = viewport.applet.getDefaultParameter( "relaxedidmatch", false); - featuresFile = new FeaturesFile(file, type).parse( + featuresFile = new FeaturesFile(file, sourceType).parse( viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { @@ -702,9 +707,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if ((viewport.getColumnSelection() != null - && viewport.getColumnSelection().getSelected() != null && viewport - .getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -732,8 +735,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hide = true; viewport.hideAllSelectedSeqs(); } - else if (!(toggleCols && viewport.getColumnSelection().getSelected() - .size() > 0)) + else if (!(toggleCols && viewport.hasSelectedColumns())) { viewport.showAllHiddenSeqs(); } @@ -741,7 +743,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { viewport.hideSelectedColumns(); if (!toggleSeqs) @@ -928,11 +930,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel.getAlignment().getAlignmentAnnotation() != null) { for (AlignmentAnnotation aa : alignPanel.getAlignment() - .getAlignmentAnnotation()) - { - boolean visible = (aa.sequenceRef == null ? showForAlignment - : showForSequences); - aa.visible = visible; + .getAlignmentAnnotation()) + { + boolean visible = (aa.sequenceRef == null ? showForAlignment + : showForSequences); + aa.visible = visible; } } alignPanel.validateAnnotationDimensions(true); @@ -1256,7 +1258,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // } else if (source == RNAHelixColour) { - new RNAHelicesColourChooser(viewport, alignPanel); + changeColour(new RNAHelicesColour(viewport.getAlignment())); + // new RNAHelicesColourChooser(viewport, alignPanel); } else if (source == modifyPID) { @@ -1359,13 +1362,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); - FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - e.getActionCommand(), viewport.getAlignment(), + fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1417,9 +1421,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, FeaturesFile formatter = new FeaturesFile(); if (format.equalsIgnoreCase("Jalview")) { - features = formatter.printJalviewFormat(viewport - .getAlignment().getSequencesArray(), - getDisplayedFeatureCols()); + features = formatter.printJalviewFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } else { @@ -1482,10 +1485,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) @@ -2233,7 +2239,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2250,7 +2259,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2619,26 +2631,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void changeColour(ColourSchemeI cs) { - - if (cs != null) - { - if (viewport.getAbovePIDThreshold()) - { - viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, - cs, "Background")); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationApplied(true); - viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } - else - { - cs.setConservationApplied(false); - } - } viewport.setGlobalColourScheme(cs); alignPanel.paintAlignment(true); @@ -2650,7 +2642,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getViewportColourScheme(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } } @@ -2661,33 +2653,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getViewportColourScheme(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } } protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.getState()); + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); + // viewport.setAbovePIDThreshold(false); + // abovePIDThreshold.setState(false); changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } public void abovePIDThreshold_actionPerformed() { - viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); - - conservationMenuItem.setState(false); - viewport.setConservationSelected(false); + boolean selected = abovePIDThreshold.getState(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + // conservationMenuItem.setState(false); + // viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } public void sortPairwiseMenuItem_actionPerformed() @@ -3232,11 +3241,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { - - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(new java.awt.event.ActionListener() { @@ -3434,7 +3441,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.colour_text")); colourTextMenuItem.addItemListener(this); displayNonconservedMenuItem.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconservedMenuItem.addItemListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); @@ -3457,45 +3464,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx")); + clustalColour.setLabel(MessageManager + .getString("label.colourScheme_clustal")); clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager.getString("label.zappo")); + zappoColour.setLabel(MessageManager + .getString("label.colourScheme_zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager.getString("label.taylor")); + taylorColour.setLabel(MessageManager + .getString("label.colourScheme_taylor")); taylorColour.addActionListener(this); hydrophobicityColour.setLabel(MessageManager - .getString("label.hydrophobicity")); + .getString("label.colourScheme_hydrophobic")); hydrophobicityColour.addActionListener(this); - helixColour - .setLabel(MessageManager.getString("label.helix_propensity")); + helixColour.setLabel(MessageManager + .getString("label.colourScheme_helix_propensity")); helixColour.addActionListener(this); strandColour.setLabel(MessageManager - .getString("label.strand_propensity")); + .getString("label.colourScheme_strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel(MessageManager.getString("label.turn_propensity")); + turnColour.setLabel(MessageManager + .getString("label.colourScheme_turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager.getString("label.buried_index")); + buriedColour.setLabel(MessageManager + .getString("label.colourScheme_buried_index")); buriedColour.addActionListener(this); purinePyrimidineColour.setLabel(MessageManager - .getString("label.purine_pyrimidine")); + .getString("label.colourScheme_purine/pyrimidine")); purinePyrimidineColour.addActionListener(this); // RNAInteractionColour.setLabel(MessageManager // .getString("label.rna_interaction")); // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager - .getString("action.by_rna_helixes")); + .getString("label.colourScheme_rna_helices")); RNAHelixColour.addActionListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); PIDColour.setLabel(MessageManager - .getString("label.percentage_identity")); + .getString("label.colourScheme_%_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel(MessageManager - .getString("label.blosum62_score")); + .getString("label.colourScheme_blosum62")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour - .setLabel(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setLabel(MessageManager + .getString("label.colourScheme_t-coffee_scores")); // it will be enabled only if a score file is provided tcoffeeColour.setEnabled(false); tcoffeeColour.addActionListener(this); @@ -3507,13 +3519,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, abovePIDThreshold.setLabel(MessageManager .getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); + modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); + modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3547,7 +3562,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.average_distance_bloslum62")); + .getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel(MessageManager .getString("label.neighbour_blosum62")); @@ -4014,19 +4029,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // resolve data source // TODO: this code should be a refactored to an io package - String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + DataSourceType protocol = AppletFormatAdapter.resolveProtocol( + pdbFile, FileFormat.PDB); if (protocol == null) { return false; } if (needtoadd) { - // make a note of the access mode and add - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - } - pdbentry.getProperty().put("protocol", protocol); + pdbentry.setProperty("protocol", protocol); toaddpdb.addPDBId(pdbentry); alignPanel.getStructureSelectionManager() .registerPDBEntry(pdbentry); @@ -4063,7 +4074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } public void newStructureView(JalviewLite applet, PDBEntry pdb, - SequenceI[] seqs, String[] chains, String protocol) + SequenceI[] seqs, String[] chains, DataSourceType protocol) { // Scrub any null sequences from the array Object[] sqch = cleanSeqChainArrays(seqs, chains); @@ -4074,10 +4085,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, System.err .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) + if (protocol == null) { - protocol = (String) pdb.getProperty().get("protocol"); + String sourceType = (String) pdb.getProperty("protocol"); + try + { + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " @@ -4100,12 +4117,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // can only do alignments with Jmol // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; - Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); + AppletJmol ajm = null, tajm; + Vector jmols = applet.getAppletWindow(AppletJmol.class); for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + tajm = (AppletJmol) jmols.elementAt(i); if (tajm.ap.alignFrame == this) { ajm = tajm; @@ -4124,7 +4140,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40;