X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2646edebaa67bfffded1fc8b276fc73611851144;hb=c9e79462a42264c560a828808934a3a156c39d0c;hp=fcdf9d2c743b05cb067251659bb466b194de0be3;hpb=781218e12641a89d5dd99906369d5b9807c1d203;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index fcdf9d2..2646ede 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -52,6 +52,8 @@ 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; @@ -62,7 +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; @@ -73,6 +75,7 @@ import jalview.structures.models.AAStructureBindingModel; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Canvas; @@ -104,7 +107,6 @@ 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; @@ -283,6 +285,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (viewport.getAlignment().isNucleotide()) { + conservationMenuItem.setEnabled(false); + clustalColour.setEnabled(false); + BLOSUM62Colour.setEnabled(false); + zappoColour.setEnabled(false); + taylorColour.setEnabled(false); + hydrophobicityColour.setEnabled(false); + helixColour.setEnabled(false); + strandColour.setEnabled(false); + turnColour.setEnabled(false); + buriedColour.setEnabled(false); viewport.updateStrucConsensus(alignPanel); if (viewport.getAlignment().hasRNAStructure()) { @@ -297,6 +309,7 @@ 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 @@ -358,14 +371,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * * @param file * file URL, content, or other resolvable path - * @param paste + * @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, DataSourceType paste, + public boolean parseFeaturesFile(String file, DataSourceType sourceType, boolean autoenabledisplay) { boolean featuresFile = false; @@ -375,7 +388,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getFeatureRenderer().getFeatureColours(); boolean relaxedIdMatching = viewport.applet.getDefaultParameter( "relaxedidmatch", false); - featuresFile = new FeaturesFile(file, paste).parse( + featuresFile = new FeaturesFile(file, sourceType).parse( viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { @@ -408,6 +421,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void keyPressed(KeyEvent evt) { + ViewportRanges ranges = viewport.getRanges(); + if (viewport.cursorMode && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt @@ -559,8 +574,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); + alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq(); } break; @@ -586,8 +601,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + alignPanel.setScrollValues(ranges.getStartRes(), + 2 * ranges.getStartSeq() - ranges.getEndSeq()); } break; @@ -598,8 +613,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + alignPanel + .setScrollValues(ranges.getStartRes(), ranges.getEndSeq()); } break; @@ -705,9 +720,7 @@ 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())) { @@ -735,8 +748,7 @@ 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(); } @@ -744,7 +756,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { viewport.hideSelectedColumns(); if (!toggleSeqs) @@ -931,11 +943,11 @@ 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); @@ -1059,6 +1071,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { delete_actionPerformed(); } + else if (source == createGroup) + { + createGroup_actionPerformed(); + } + else if (source == unGroup) + { + unGroup_actionPerformed(); + } else if (source == grpsFromSelection) { makeGrpsFromSelection_actionPerformed(); @@ -1259,7 +1279,8 @@ 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) { @@ -1366,7 +1387,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); - FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); @@ -1420,9 +1442,8 @@ 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 { @@ -1485,10 +1506,13 @@ 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) @@ -2050,7 +2074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment())); - viewport.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight()); viewport.getAlignment().getWidth(); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2286,6 +2310,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void trimAlignment(boolean trimLeft) { + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); ColumnSelection colSel = viewport.getColumnSelection(); int column; @@ -2308,20 +2334,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - seqs = viewport.getAlignment().getSequencesArray(); + seqs = al.getSequencesArray(); } TrimRegionCommand trimRegion; if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, - column, viewport.getAlignment()); - viewport.setStartRes(0); + column, al); + ranges.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", false, seqs, - column, viewport.getAlignment()); + column, al); } statusBar.setText(MessageManager.formatMessage( @@ -2330,23 +2356,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .toString() })); addHistoryItem(trimRegion); - for (SequenceGroup sg : viewport.getAlignment().getGroups()) + for (SequenceGroup sg : al.getGroups()) { if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.getAlignment().deleteGroup(sg); + al.deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, al.getSequences()); } } public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.getAlignment().getWidth() - 1; + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) @@ -2374,22 +2402,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + ranges.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, al.getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.getAlignment().getWidth() - 1; + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) @@ -2406,16 +2436,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.getAlignment())); + al)); - viewport.setStartRes(seq.findIndex(startRes) - 1); + ranges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, al.getSequences()); } @@ -2628,26 +2657,6 @@ 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); @@ -2659,7 +2668,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } } @@ -2670,33 +2679,51 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } } protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.getState()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); 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); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } public void sortPairwiseMenuItem_actionPerformed() @@ -3241,7 +3268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { MenuItem item = new MenuItem(ff); @@ -3319,7 +3346,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); + createGroup.addActionListener(this); unGroup.setLabel(MessageManager.getString("action.remove_group")); + unGroup.addActionListener(this); + annotationColumnSelection.setLabel(MessageManager .getString("action.select_by_annotation")); annotationColumnSelection.addActionListener(this); @@ -3441,7 +3471,7 @@ 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); @@ -3464,45 +3494,50 @@ 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); @@ -3514,13 +3549,16 @@ 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_threshold")); + modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager .getString("label.modify_conservation_threshold")); + modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3554,7 +3592,7 @@ 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")); @@ -4029,12 +4067,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (needtoadd) { - // make a note of the access mode and add - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - } - pdbentry.getProperty().put("protocol", protocol.toString()); + pdbentry.setProperty("protocol", protocol); toaddpdb.addPDBId(pdbentry); alignPanel.getStructureSelectionManager() .registerPDBEntry(pdbentry); @@ -4084,7 +4117,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (protocol == null) { - String sourceType = pdb.getProperty().get("protocol"); + String sourceType = (String) pdb.getProperty("protocol"); try { protocol = DataSourceType.valueOf(sourceType);