X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=c1bbc8d58d0167bab19eb405f995533f9ee27a1b;hb=3eef76298c55f3def21eed2516b5ace4405bed0a;hp=e812530c901193acb574caba11c06a5b8fd4142e;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e812530..c1bbc8d 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -255,29 +255,29 @@ public class PopupMenu extends JPopupMenu } else { - if (ap.av.alignment.isNucleotide() == false) + if (ap.av.getAlignment().isNucleotide() == false) { structureMenu.remove(viewStructureMenu); } // structureMenu.remove(colStructureMenu); } - if (ap.av.alignment.isNucleotide() == true) + if (ap.av.getAlignment().isNucleotide() == true) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { if (aa[i].getRNAStruc() != null) { final String rnastruc = aa[i].getRNAStruc(); - + final String structureLine=aa[i].label; menuItem = new JMenuItem(); - menuItem.setText("RNA structure - consensus"); + menuItem.setText("2D RNA "+structureLine); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - new AppVarna(seq.getSequenceAsString(), rnastruc, seq + new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq .getName(), ap); } }); @@ -298,13 +298,13 @@ public class PopupMenu extends JPopupMenu // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText("RNA structure - "+seq.getName()); + menuItem.setText("2D RNA - "+seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - new AppVarna(seq.getSequenceAsString(), rnastruc, seq + new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq .getName(), ap); } }); @@ -340,9 +340,9 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows) + if (ap.av.hasHiddenRows()) { - final int index = ap.av.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) @@ -364,7 +364,7 @@ public class PopupMenu extends JPopupMenu } } // for the case when no sequences are even visible - if (ap.av.hasHiddenRows) { + if (ap.av.hasHiddenRows()) { { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() @@ -506,7 +506,7 @@ public class PopupMenu extends JPopupMenu editMenu.setVisible(false); } - if (!ap.av.alignment.getGroups().contains(sg)) + if (!ap.av.getAlignment().getGroups().contains(sg)) { unGroupMenuItem.setVisible(false); } @@ -1289,8 +1289,7 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.hiddenRepSequences), - ap.av.alignment.getWidth()); + sg,ap.av.getHiddenRepSequences()); refresh(); } @@ -1417,7 +1416,7 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() @@ -1471,7 +1470,7 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1489,7 +1488,7 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); @@ -1525,11 +1524,11 @@ public class PopupMenu extends JPopupMenu { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1599,7 +1598,7 @@ public class PopupMenu extends JPopupMenu // this method won't add a new group if it already exists if (sg != null) { - ap.av.alignment.addGroup(sg); + ap.av.getAlignment().addGroup(sg); } return sg; @@ -1653,7 +1652,7 @@ public class PopupMenu extends JPopupMenu void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); refresh(); } @@ -1807,7 +1806,7 @@ public class PopupMenu extends JPopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1834,7 +1833,7 @@ public class PopupMenu extends JPopupMenu ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1883,9 +1882,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[] + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() @@ -1954,10 +1953,10 @@ public class PopupMenu extends JPopupMenu AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); - ap.av.alignment.addAnnotation(an); + ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an, 0); + ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); @@ -1984,8 +1983,8 @@ public class PopupMenu extends JPopupMenu EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), - sg.getSequencesAsArray(ap.av.hiddenRepSequences), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand);