X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=78c175b3c062a0d42abc35657f3209469cd5667c;hb=60b22c7b9ccf824a85fa2761e34dfdfba415a8a1;hp=c4c2c5bf13fe9d20e6a92efb6e9c2817405d031d;hpb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index c4c2c5b..78c175b 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -38,7 +38,8 @@ public class AlignFrame extends Frame implements ActionListener, public AlignViewport viewport; int NEW_WINDOW_WIDTH = 700; int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + + String jalviewServletURL; public AlignFrame(AlignmentI al, @@ -46,6 +47,9 @@ public class AlignFrame extends Frame implements ActionListener, String title, boolean embedded) { + + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + try{ jbInit(); }catch(Exception ex) @@ -53,12 +57,13 @@ public class AlignFrame extends Frame implements ActionListener, ex.printStackTrace(); } - this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); annotationPanelMenuItem.setState(viewport.showAnnotation); + seqLimits.setState(viewport.showJVSuffix); + if(applet!=null) { String param = applet.getParameter("sortBy"); @@ -105,6 +110,8 @@ public class AlignFrame extends Frame implements ActionListener, this.addKeyListener(this); alignPanel.seqPanel.seqCanvas.addKeyListener(this); alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() { @@ -148,162 +155,35 @@ public class AlignFrame extends Frame implements ActionListener, * @param String DOCUMENT ME! */ - public void parseFeaturesFile(String file) + public void parseFeaturesFile(String file, String type) { - String line = null; - try - { - BufferedReader in = null; - java.io.InputStream is = getClass().getResourceAsStream("/" + file); - if (is != null) - { - in = new BufferedReader(new java.io.InputStreamReader(is)); - } - else - { - URL url = new URL(file); - in = new BufferedReader(new InputStreamReader(url.openStream())); - } - - SequenceI seq = null; - String type, desc, token; - - int index, start, end; - StringTokenizer st; - SequenceFeature sf; - FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - String featureGroup = null, groupLink = null; - Hashtable typeLink = new Hashtable(); - - while ( (line = in.readLine()) != null) - { - st = new StringTokenizer(line, "\t"); - if(!st.hasMoreTokens()) - continue; - - if (st.countTokens() < 4) - { - type = st.nextToken(); - if(type.equalsIgnoreCase("startgroup")) - { - featureGroup = st.nextToken(); - if (st.hasMoreElements()) - { - groupLink = st.nextToken(); - fr.addFeatureLink(featureGroup, groupLink); - } - } - else if(type.equalsIgnoreCase("endgroup")) - { - //We should check whether this is the current group, - //but at present theres no way of showing more than 1 group - st.nextToken(); - featureGroup = null; - groupLink = null; - } - else - { - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - fr.setColour(type, ucs.findColour("A")); - if (st.hasMoreElements()) - { - String link = st.nextToken(); - typeLink.put(type, link); - fr.addFeatureLink(type, link); - } - - } - continue; - } - - while (st.hasMoreElements()) - { - desc = st.nextToken(); - - token = st.nextToken(); - if (!token.equals("ID_NOT_SPECIFIED")) - { - index = viewport.alignment.findIndex(viewport.alignment.findName( - token)); - st.nextToken(); - } - else - { - index = Integer.parseInt(st.nextToken()); - } - - start = Integer.parseInt(st.nextToken()); - end = Integer.parseInt(st.nextToken()); - - seq = viewport.alignment.getSequenceAt(index); - - type = st.nextToken(); - - if(fr.getColour(type)==null) - { - // Probably the old style groups file - UserColourScheme ucs = new UserColourScheme(type); - fr.setColour(type, ucs.findColour("A")); - } - - sf = new SequenceFeature(type, desc, start, end, 0f, featureGroup); - seq.addSequenceFeature(sf); - - if(groupLink!=null) - { - sf.addLink(groupLink); - sf.description += "%LINK%"; - } - if(typeLink.containsKey(type)) - { - sf.addLink(typeLink.get(type).toString()); - sf.description += "%LINK%"; - } - - parseDescriptionHTML(sf); - } - } - - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - - alignPanel.repaint(); - + Hashtable featureLinks = new Hashtable(); + boolean featuresFile = false; + try{ + featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas. + getFeatureRenderer().featureColours, + featureLinks, + true); } - catch (Exception ex) + catch(Exception ex) { ex.printStackTrace(); - System.out.println("Error parsing groups file: " + ex +"\n"+line); } - } - void parseDescriptionHTML(SequenceFeature sf) - { - StringBuffer sb = new StringBuffer(); - StringTokenizer st = new StringTokenizer(sf.getDescription(), "<"); - String token, link; - while(st.hasMoreElements()) + if(featuresFile) { - token = st.nextToken("<>"); - if(token.equalsIgnoreCase("html") || token.startsWith("/")) - continue; - - if(token.startsWith("a href=")) - { - link = token.substring(token.indexOf("\"")+1, token.length()-1); - String label = st.nextToken("<>"); - sf.addLink(label+"|"+link); - sb.append(label+"%LINK%"); - } - else if(token.equalsIgnoreCase("br")) - sb.append("\n"); - else - sb.append(token); + if(featureLinks.size()>0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + alignPanel.repaint(); } - sf.description = sb.toString(); } + public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -325,7 +205,7 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: - if (viewport.cursorMode) + if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.seqPanel.setCursorColumn(); } @@ -449,6 +329,40 @@ public class AlignFrame extends Frame implements ActionListener, findMenuItem_actionPerformed(); } break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if(toggleSeqs) + { + if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + viewport.showAllHiddenSeqs(); + } + + if(toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if(!toggleSeqs) + viewport.selectionGroup = sg; + } + else if (!hide) + viewport.showAllHiddenColumns(); + } + + alignPanel.repaint(); + break; + } + } } public void keyReleased(KeyEvent evt) @@ -494,115 +408,137 @@ public void itemStateChanged(ItemEvent evt) } public void actionPerformed(ActionEvent evt) { - if(evt.getSource()==inputText) + Object source = evt.getSource(); + + if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==loadTree) + else if(source==loadTree) loadTree_actionPerformed(); - else if(evt.getSource()==closeMenuItem) + else if(source==loadApplication) + launchFullApplication(); + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==inputText) + else if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==closeMenuItem) + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==pasteNew) + else if(source==pasteNew) pasteNew_actionPerformed(); - else if(evt.getSource()==pasteThis) + else if(source==pasteThis) pasteThis_actionPerformed(); - else if(evt.getSource()==cut) + else if(source==cut) cut_actionPerformed(); - else if(evt.getSource()==delete) + else if(source==delete) delete_actionPerformed(); - else if(evt.getSource()==deleteGroups) + else if(source==deleteGroups) deleteGroups_actionPerformed(); - else if(evt.getSource()==selectAllSequenceMenuItem) + else if(source==selectAllSequenceMenuItem) selectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==deselectAllSequenceMenuItem) + else if(source==deselectAllSequenceMenuItem) deselectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==invertSequenceMenuItem) + else if(source==invertSequenceMenuItem) invertSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==remove2LeftMenuItem) + else if(source==invertColSel) + { viewport.invertColumnSelection(); alignPanel.repaint(); } + else if(source==remove2LeftMenuItem) remove2LeftMenuItem_actionPerformed(); - else if(evt.getSource()==remove2RightMenuItem) + else if(source==remove2RightMenuItem) remove2RightMenuItem_actionPerformed(); - else if(evt.getSource()==removeGappedColumnMenuItem) + else if(source==removeGappedColumnMenuItem) removeGappedColumnMenuItem_actionPerformed(); - else if(evt.getSource()==removeAllGapsMenuItem) + else if(source==removeAllGapsMenuItem) removeAllGapsMenuItem_actionPerformed(); - else if(evt.getSource()==findMenuItem) + else if(source==findMenuItem) findMenuItem_actionPerformed(); - else if(evt.getSource()==font) + else if(source==font) font_actionPerformed(); - else if(evt.getSource()==featureSettings) + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); alignPanel.repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); alignPanel.repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + viewport.hideAllSelectedSeqs(); + } + else if(source==featureSettings) featureSettings_actionPerformed(); - else if(evt.getSource()==overviewMenuItem) + else if(source==overviewMenuItem) overviewMenuItem_actionPerformed(); - else if(evt.getSource()==noColourmenuItem) + else if(source==noColourmenuItem) noColourmenuItem_actionPerformed(); - else if(evt.getSource()==clustalColour) + else if(source==clustalColour) clustalColour_actionPerformed(); - else if(evt.getSource()==zappoColour) + else if(source==zappoColour) zappoColour_actionPerformed(); - else if(evt.getSource()==taylorColour) + else if(source==taylorColour) taylorColour_actionPerformed(); - else if(evt.getSource()==hydrophobicityColour) + else if(source==hydrophobicityColour) hydrophobicityColour_actionPerformed(); - else if(evt.getSource()==helixColour) + else if(source==helixColour) helixColour_actionPerformed(); - else if(evt.getSource()==strandColour) + else if(source==strandColour) strandColour_actionPerformed(); - else if(evt.getSource()==turnColour) + else if(source==turnColour) turnColour_actionPerformed(); - else if(evt.getSource()==buriedColour) + else if(source==buriedColour) buriedColour_actionPerformed(); - else if(evt.getSource()==nucleotideColour) + else if(source==nucleotideColour) nucleotideColour_actionPerformed(); - else if(evt.getSource()==modifyPID) + else if(source==modifyPID) modifyPID_actionPerformed(); - else if(evt.getSource()==modifyConservation) + else if(source==modifyConservation) modifyConservation_actionPerformed(); - else if(evt.getSource()==userDefinedColour) + else if(source==userDefinedColour) userDefinedColour_actionPerformed(); - else if(evt.getSource()==PIDColour) + else if(source==PIDColour) PIDColour_actionPerformed(); - else if(evt.getSource()==BLOSUM62Colour) + else if(source==BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); - else if(evt.getSource()==annotationColour) + else if(source==annotationColour) new AnnotationColourChooser(viewport, alignPanel); - else if(evt.getSource()==sortPairwiseMenuItem) + else if(source==sortPairwiseMenuItem) sortPairwiseMenuItem_actionPerformed(); - else if(evt.getSource()==sortIDMenuItem) + else if(source==sortIDMenuItem) sortIDMenuItem_actionPerformed(); - else if(evt.getSource()==sortGroupMenuItem) + else if(source==sortGroupMenuItem) sortGroupMenuItem_actionPerformed(); - else if(evt.getSource()==removeRedundancyMenuItem) + else if(source==removeRedundancyMenuItem) removeRedundancyMenuItem_actionPerformed(); - else if(evt.getSource()==pairwiseAlignmentMenuItem) + else if(source==pairwiseAlignmentMenuItem) pairwiseAlignmentMenuItem_actionPerformed(); - else if(evt.getSource()==PCAMenuItem) + else if(source==PCAMenuItem) PCAMenuItem_actionPerformed(); - else if(evt.getSource()==averageDistanceTreeMenuItem) + else if(source==averageDistanceTreeMenuItem) averageDistanceTreeMenuItem_actionPerformed(); - else if(evt.getSource()==neighbourTreeMenuItem) + else if(source==neighbourTreeMenuItem) neighbourTreeMenuItem_actionPerformed(); - else if(evt.getSource()==njTreeBlosumMenuItem) + else if(source==njTreeBlosumMenuItem) njTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==avDistanceTreeBlosumMenuItem) + else if(source==avDistanceTreeBlosumMenuItem) avTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==documentation) + else if(source==documentation) documentation_actionPerformed(); - else if(evt.getSource()==about) + else if(source==about) about_actionPerformed(); } @@ -628,10 +564,73 @@ public void itemStateChanged(ItemEvent evt) viewport.showJVSuffix)); } + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open="+ + appendProtocol( viewport.applet.getParameter("file") ) ); + + if(viewport.applet.getParameter("features")!=null) + { + url.append( "&features=" ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + } + + if(viewport.applet.getParameter("annotations")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + } + + if(viewport.applet.getParameter("defaultColour")!=null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) + ); + } + + if(viewport.applet.getParameter("userDefinedColour")!=null) + { + url.append( "&colour=" + + removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) + ); + } + + showURL(url.toString(), "FULL_APP"); + } + + + String removeWhiteSpace(String colour) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < colour.length(); i++) + { + if (Character.isWhitespace(colour.charAt(i))) + sb.append("%20"); + else + sb.append(colour.charAt(i)); + } + + return sb.toString(); + } + + + String appendProtocol(String url) + { + try{ + new URL(url); + }catch(java.net.MalformedURLException ex) + { + url = viewport.applet.getCodeBase()+url; + } + return url; + } + public void closeMenuItem_actionPerformed() { PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && applet==null) + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); this.dispose(); @@ -670,21 +669,28 @@ public void itemStateChanged(ItemEvent evt) public void addHistoryItem(HistoryItem hi) { historyList.push(hi); + redoList.removeAllElements(); updateEditMenuBar(); } protected void undoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem nh,hi = (HistoryItem) historyList.pop(); + redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); restoreHistoryItem(hi); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } protected void redoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) redoList.pop(); + HistoryItem nh,hi = (HistoryItem) redoList.pop(); + historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); restoreHistoryItem(hi); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -693,8 +699,7 @@ public void itemStateChanged(ItemEvent evt) // used by undo and redo void restoreHistoryItem(HistoryItem hi) { - hi.restore(); - + hi.restore(viewport.getColumnSelection()); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -713,13 +718,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(false).contains(temp)) { continue; } @@ -733,13 +738,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(true).contains(temp)) { continue; } @@ -752,7 +757,8 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } - StringBuffer copiedSequences; + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -763,7 +769,7 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -773,7 +779,26 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(); i++) + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) + { + int[] region = (int[]) + viewport.getColumnSelection().getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); + } + } + else + copiedHiddenColumns = null; + + + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = null; @@ -881,9 +906,18 @@ public void itemStateChanged(ItemEvent evt) newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), - applet, + viewport.applet, newtitle, false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); @@ -919,10 +953,10 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) + if(sg.getSize(false)==viewport.alignment.getHeight()) allSequences = true; - for (int i = 0; i < sg.sequences.size(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.getAlignment().findIndex(seq); @@ -1015,12 +1049,13 @@ public void itemStateChanged(ItemEvent evt) ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, HistoryItem.HIDE)); int min = colSel.getMin(); viewport.getAlignment().trimLeft(min); colSel.compensateForEdit(0, min); - + edit.addShift(0, min); if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveLeft(min); @@ -1048,6 +1083,7 @@ public void itemStateChanged(ItemEvent evt) HistoryItem.HIDE)); int max = colSel.getMax(); viewport.getAlignment().trimRight(max); + if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveRight(max); @@ -1069,7 +1105,8 @@ public void itemStateChanged(ItemEvent evt) public void removeGappedColumnMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gapped Columns", + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); @@ -1087,7 +1124,10 @@ public void itemStateChanged(ItemEvent evt) public void removeAllGapsMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, + // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences + // TODO: columnSelection.compensateforedits should be called (and passed to history item) + HistoryItem editgaps; + addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); //This is to maintain viewport position on first residue @@ -1096,68 +1136,57 @@ public void itemStateChanged(ItemEvent evt) int startRes = seq.findPosition(viewport.startRes); SequenceI current; - int jSize; - Vector seqs=null; int start=0, end = viewport.alignment.getWidth(); if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + && viewport.getSelectionGroup().getSequences(false) != null + && viewport.getSelectionGroup().getSize(false)>0) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequences(true); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes()+1; } else seqs = viewport.alignment.getSequences(); + /* Commented out regions below are partial implementation of todo above. + * divide start,end into visible chunks, and for each: + int diff=end-start+1; + int diffmax=0; + int dr[] = new int[seqs.size()]; + */ for (int i = 0; i < seqs.size(); i++) { current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); - - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; - - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - if(rangeStart==-1) - { - rangeStart = j; - rangeEnd = j+1; - } - else - { - rangeEnd++; - } - j++; - } - else - { - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - j-=rangeEnd-rangeStart; - jSize-=rangeEnd-rangeStart; - rangeStart = -1; - rangeEnd = -1; - } - else - j++; - } - } - while (j < end && j < jSize); - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - } + //dr[i]= + current.removeGaps(start, end); + /*if (d0) { + // record shift for history. + editgaps.addShift(start, diff); + if (viewport.hasHiddenColumns && diffmax>diff) { + // pad sequence + StringBuffer gaps=new StringBuffer(diffmax); + for (int i=0,j=diffmax-diff; i0) { + String sq = current.getSequence(); + current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); + } + } + } + }*/ + viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } @@ -1212,7 +1241,8 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); + ((ClustalxColourScheme)sg.cs).resetClustalX( + sg.getSequences(true), sg.getWidth()); } sg.recalcConservation(); } @@ -1255,6 +1285,7 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } + protected void scaleAbove_actionPerformed() { viewport.setScaleAboveWrapped(scaleAbove.getState()); @@ -1448,7 +1479,7 @@ public void itemStateChanged(ItemEvent evt) } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -1468,7 +1499,7 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1477,7 +1508,7 @@ public void itemStateChanged(ItemEvent evt) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1590,17 +1621,13 @@ public void itemStateChanged(ItemEvent evt) public void removeRedundancyMenuItem_actionPerformed() { - RedundancyPanel sp = new RedundancyPanel(alignPanel); - Frame frame = new Frame(); - frame.add(sp); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 120); - + new RedundancyPanel(alignPanel); } public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1630,8 +1657,8 @@ public void itemStateChanged(ItemEvent evt) } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) + viewport.getSelectionGroup().getSize(false) < 4 && + viewport.getSelectionGroup().getSize(false) > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1689,29 +1716,23 @@ public void itemStateChanged(ItemEvent evt) } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize(false) > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } + final TreePanel tp = new TreePanel(viewport, + type, + pwType); - addTreeMenuItem(tp, title); + addTreeMenuItem(tp, title); - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + } } void loadTree_actionPerformed() { - TreePanel tp = null; - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); cap.setText("Paste your Newick tree file here."); cap.treeImport = true; @@ -1723,8 +1744,9 @@ public void itemStateChanged(ItemEvent evt) public void loadTree(jalview.io.NewickFile tree, String treeFile) { TreePanel tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), - tree, "From File - ", treeFile); + treeFile, + "From File - ", + tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -1825,7 +1847,7 @@ public void itemStateChanged(ItemEvent evt) public void showURL(String url, String target) { - if (applet == null) + if (viewport.applet == null) { System.out.println("Not running as applet - no browser available."); } @@ -1833,7 +1855,8 @@ public void itemStateChanged(ItemEvent evt) { try { - applet.getAppletContext().showDocument(new java.net.URL(url), + System.out.println("Show url: "+url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), target); } catch (Exception ex) @@ -1849,6 +1872,7 @@ public void itemStateChanged(ItemEvent evt) protected MenuBar alignFrameMenuBar = new MenuBar(); protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); protected MenuItem loadTree = new MenuItem("Load Associated Tree"); protected MenuItem closeMenuItem = new MenuItem("Close"); protected Menu editMenu = new Menu("Edit"); @@ -1942,12 +1966,11 @@ public void itemStateChanged(ItemEvent evt) MenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { - item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. - elementAt( - i)); + item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1959,6 +1982,7 @@ public void itemStateChanged(ItemEvent evt) outputTextboxMenu.add(item); } closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); @@ -2114,6 +2138,20 @@ public void itemStateChanged(ItemEvent evt) sequenceFeatures.setState(false); annotationColour.setLabel("by Annotation..."); annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -2124,6 +2162,8 @@ public void itemStateChanged(ItemEvent evt) alignFrameMenuBar.add(helpMenu); fileMenu.add(inputText); fileMenu.add(outputTextboxMenu); + if(jalviewServletURL!=null) + fileMenu.add(loadApplication); fileMenu.addSeparator(); fileMenu.add(loadTree); fileMenu.add(closeMenuItem); @@ -2137,7 +2177,8 @@ public void itemStateChanged(ItemEvent evt) editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); + editMenu.add(invertColSel); + editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); @@ -2147,13 +2188,15 @@ public void itemStateChanged(ItemEvent evt) searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); viewMenu.addSeparator(); + viewMenu.add(seqLimits); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); @@ -2204,6 +2247,10 @@ public void itemStateChanged(ItemEvent evt) calculate.add(njTreeBlosumMenuItem); helpMenu.add(documentation); helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); } public void setEmbedded() @@ -2254,18 +2301,18 @@ public void itemStateChanged(ItemEvent evt) // setVisible(false); fileMenu.remove(closeMenuItem); - fileMenu.remove(2); // Seperator + fileMenu.remove(3); // Seperator - applet.setLayout(new BorderLayout()); - applet.add(embeddedMenu, BorderLayout.NORTH); - applet.add(statusBar, BorderLayout.SOUTH); - // applet.validate(); + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + // viewport.applet.validate(); - alignPanel.setSize(applet.size().width, applet.size().height + alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); - applet.add(alignPanel, BorderLayout.CENTER); - applet.validate(); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); } @@ -2276,6 +2323,13 @@ public void itemStateChanged(ItemEvent evt) MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); public void mousePressed(MouseEvent evt) {