X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=8f1836cfe60b48f1dcd4cc8779106c72a3eda992;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=dca9da4a84e744d2f704510390172c8bc4009d25;hpb=c97c8a9e4fd58a4927e040e314c5be3c5356745e;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index dca9da4..8f1836c 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -26,6 +26,7 @@ import java.util.Vector; import jalview.analysis.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.commands.ChangeCaseCommand; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener @@ -64,9 +65,15 @@ public class APopupMenu MenuItem pdb = new MenuItem(); MenuItem hideSeqs = new MenuItem(); MenuItem repGroup = new MenuItem(); + MenuItem sequenceName = new MenuItem("Edit Name/Description"); Sequence seq; MenuItem revealAll = new MenuItem(); + Menu menu1 = new Menu(); + + Dialog editNameDialog; + Button okDialog = new Button("Accept"); + Button cancelDialog = new Button("Cancel");; public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { @@ -99,7 +106,7 @@ public class APopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null && sg.getSize(false)>0) + if (sg != null && sg.getSize()>0) { showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); @@ -143,7 +150,6 @@ public class APopupMenu else url = link.substring(link.lastIndexOf("|")+1); - System.out.println("add "+url +" "+target); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -217,6 +223,14 @@ public class APopupMenu else if (source == unGroupMenuItem) unGroupMenuItem_actionPerformed(); + else if(source == sequenceName) + editName(); + else if (source==okDialog || source==cancelDialog) + { + editNameDialog.setVisible(false); + if(source==cancelDialog) + editNameDialog = null; + } else if(source == pdb) addPDB(); else if(source == hideSeqs) @@ -234,43 +248,75 @@ public class APopupMenu ap.alignFrame.cut_actionPerformed(); else if(source==toUpper || source==toLower || source==toggleCase) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do { - for (int g = 0; g < sg.getSize(true); g++) + if (ap.av.hasHiddenColumns) + { + if(start==0) + start = ap.av.colSel.adjustForHiddenColumns(start); + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; + } + + regions.addElement(new int[] + {start, end}); + + if (ap.av.hasHiddenColumns) { - int start = sg.getStartRes(); - int end = sg.getEndRes() + 1; - - do - { - if (ap.av.hasHiddenColumns) - { - end = ap.av.colSel.getHiddenBoundaryRight(start); - if (start == end) - end = sg.getEndRes() + 1; - if (end > sg.getEndRes()) - end = sg.getEndRes() + 1; - } - - if (source == toggleCase) - ( (SequenceI) sg.getSequences(true).elementAt(g)) - .toggleCase(start, end); - else - ( (SequenceI) sg.getSequences(true).elementAt(g)) - .changeCase(source == toUpper, start, end); - - if (ap.av.hasHiddenColumns) - { - start = ap.av.colSel.adjustForHiddenColumns(end); - start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; - } - - } - while (end < sg.getEndRes()); + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; } - ap.seqPanel.seqCanvas.repaint(); } + while (end < sg.getEndRes()); + + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } + + + String description; + int caseChange; + + if(source==toggleCase) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if(source==toUpper) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + + } } else outputText(evt); @@ -279,23 +325,7 @@ public class APopupMenu void outputText(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); - Vector vseqs = new Vector(); - - String [] selection = ap.av.getViewAsString(true); - SequenceI [] seqs = ap.av.getSelectionAsNewSequence(); - if (selection != null) - { - for (int i = 0; i < selection.length; i++) - { - Sequence seq = new Sequence( - seqs[i].getName(), - selection[i], - seqs[i].getStart(), seqs[i].getEnd()); - seq.setDescription(seqs[i].getDescription()); - vseqs.addElement( seq ); - } - } + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); @@ -305,11 +335,54 @@ public class APopupMenu cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( e.getActionCommand(), - vseqs, + new Alignment( ap.av.getSelectionAsNewSequence() ), ap.av.showJVSuffix)); } + void editName() + { + TextField id = new TextField(seq.getName(), 40); + TextField description = new TextField(seq.getDescription(), 40); + Panel panel = new Panel(new BorderLayout()); + Panel panel2 = new Panel(new BorderLayout()); + panel2.add(new Label(" Sequence Name "), BorderLayout.WEST); + panel2.add(id, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.NORTH); + panel2 = new Panel(new BorderLayout()); + panel2.add(new Label("Sequence Description "), BorderLayout.WEST); + panel2.add(description, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.CENTER); + + panel2 = new Panel(new FlowLayout()); + + panel2.add(okDialog); + panel2.add(cancelDialog); + + panel.add(panel2, BorderLayout.SOUTH); + + editNameDialog = new Dialog(ap.alignFrame, + "Edit Sequence Name / Description", + true); + + editNameDialog.add(panel, BorderLayout.NORTH); + + editNameDialog.setBounds(ap.alignFrame.getBounds().x + +(ap.alignFrame.getSize().width-500)/2 , + ap.alignFrame.getBounds().y + +(ap.alignFrame.getSize().height-120)/2, + 500, 120); + + editNameDialog.show(); + + if (editNameDialog != null) + { + seq.setName(id.getText()); + seq.setDescription(description.getText()); + ap.repaint(); + } + } + void addPDB() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); @@ -337,6 +410,7 @@ public class APopupMenu showBoxes.setLabel("Boxes"); showBoxes.setState(true); showBoxes.addItemListener(this); + sequenceName.addActionListener(this); showText.setLabel("Text"); showText.addItemListener(this); @@ -348,19 +422,14 @@ public class APopupMenu hideSeqs.setLabel("Hide Sequences"); repGroup.setLabel("Represent Group with"); revealAll.setLabel("Reveal All"); - + menu1.setLabel("Group"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); this.add(revealAll); groupMenu.add(editMenu); groupMenu.add(outputmenu); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); + groupMenu.add(menu1); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -416,13 +485,21 @@ public class APopupMenu editMenu.add(toLower); toLower.addActionListener(this); editMenu.add(toggleCase); + seqMenu.add(sequenceName); seqMenu.add(pdb); seqMenu.add(repGroup); + menu1.add(unGroupMenuItem); + menu1.add(colourMenu); + menu1.add(showBoxes); + menu1.add(showText); + menu1.add(showColourText); toggleCase.addActionListener(this); pdb.addActionListener(this); hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + okDialog.addActionListener(this); + cancelDialog.addActionListener(this); } @@ -436,7 +513,8 @@ public class APopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } @@ -496,7 +574,7 @@ public class APopupMenu if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -524,7 +602,7 @@ public class APopupMenu { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); } @@ -535,7 +613,7 @@ public class APopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); @@ -558,7 +636,7 @@ public class APopupMenu Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), 0, + sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -618,34 +696,33 @@ public class APopupMenu void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize(false)<1) + if(sg==null || sg.getSize()<1) { ap.av.hideSequence(new SequenceI[]{seq}); return; } - int gsize = sg.getSize(false); - SequenceI [] hseqs; + ap.av.setSelectionGroup(null); - hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ]; + if (representGroup) + { + ap.av.hideRepSequences(seq, sg); - int index = 0; - for(int i=0; i