X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=78c175b3c062a0d42abc35657f3209469cd5667c;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=d1b2da99185f0add4f6f9999011ebd774f18a772;hpb=8f599b2d8da5ad8ccfcd42139e1b6f170bc3ad0f;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index d1b2da9..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 +38,6 @@ 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; @@ -58,7 +57,6 @@ public class AlignFrame extends Frame implements ActionListener, ex.printStackTrace(); } - this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); @@ -112,6 +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() { @@ -329,6 +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) @@ -374,117 +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()==loadApplication) + else if(source==loadApplication) launchFullApplication(); - else if(evt.getSource()==closeMenuItem) + 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(); } @@ -515,25 +569,31 @@ public void itemStateChanged(ItemEvent evt) StringBuffer url = new StringBuffer(jalviewServletURL); url.append("?open="+ - appendProtocol( applet.getParameter("file") ) ); + appendProtocol( viewport.applet.getParameter("file") ) ); - if(applet.getParameter("features")!=null) + if(viewport.applet.getParameter("features")!=null) { url.append( "&features=" ); - url.append( appendProtocol( applet.getParameter("features") ) ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); } - if(applet.getParameter("defaultColour")!=null) + 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(applet.getParameter("defaultColour")) + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) ); } - if(applet.getParameter("userDefinedColour")!=null) + if(viewport.applet.getParameter("userDefinedColour")!=null) { url.append( "&colour=" + - removeWhiteSpace( applet.getParameter("userDefinedColour") ) + removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) ); } @@ -562,7 +622,7 @@ public void itemStateChanged(ItemEvent evt) new URL(url); }catch(java.net.MalformedURLException ex) { - url = applet.getCodeBase()+url; + url = viewport.applet.getCodeBase()+url; } return url; } @@ -570,7 +630,7 @@ public void itemStateChanged(ItemEvent evt) 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(); @@ -609,21 +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()); @@ -632,8 +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()); @@ -691,7 +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) @@ -712,6 +779,25 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; + 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; @@ -820,9 +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); @@ -954,12 +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); @@ -987,6 +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); @@ -1008,7 +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)); @@ -1026,7 +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 @@ -1035,8 +1136,6 @@ 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(); @@ -1052,51 +1151,42 @@ public void itemStateChanged(ItemEvent evt) 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()); } @@ -1195,6 +1285,7 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } + protected void scaleAbove_actionPerformed() { viewport.setScaleAboveWrapped(scaleAbove.getState()); @@ -1535,7 +1626,8 @@ public void itemStateChanged(ItemEvent evt) public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize(false) > 1) + if (viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1624,25 +1716,19 @@ public void itemStateChanged(ItemEvent evt) } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) > 3) - { - tp = new TreePanel(viewport, - viewport.getSelectionGroup().getSequences(false), - 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() @@ -1658,8 +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); } @@ -1760,7 +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."); } @@ -1769,7 +1856,7 @@ public void itemStateChanged(ItemEvent evt) try { System.out.println("Show url: "+url); - applet.getAppletContext().showDocument(new java.net.URL(url), + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), target); } catch (Exception ex) @@ -1879,12 +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) @@ -2052,6 +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); @@ -2077,7 +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); @@ -2087,13 +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); @@ -2144,6 +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() @@ -2196,16 +2303,16 @@ public void itemStateChanged(ItemEvent evt) fileMenu.remove(closeMenuItem); 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(); } @@ -2216,6 +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) {