X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=b07dce8c38ad66fe6221a94952380c4b76cf0d75;hb=31a5f9724e7ba5c8f67a6db9a0c0f2356cd81b9d;hp=a1007bb73a658667758a45c2c1ca72089e4174b3;hpb=dfb0a0fc461353af5800d46078816f5d43720edc;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index a1007bb..b07dce8 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -3,6 +3,7 @@ package jalview.gui; import jalview.datamodel.*; import jalview.analysis.*; import jalview.schemes.*; +import java.awt.*; import javax.swing.*; import java.awt.event.*; import jalview.io.*; @@ -11,9 +12,6 @@ import MCview.*; public class PopupMenu extends JPopupMenu { JMenu groupMenu = new JMenu(); - JMenuItem copyGroup = new JMenuItem(); - JMenuItem moveGroup = new JMenuItem(); - JMenuItem deleteSequences = new JMenuItem(); JMenuItem analyze = new JMenuItem(); JMenu defineMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -43,6 +41,7 @@ public class PopupMenu extends JPopupMenu Sequence sequence; JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem pdbMenuItem = new JMenuItem(); + JMenuItem outline = new JMenuItem(); public PopupMenu(AlignmentPanel ap, Sequence seq) { @@ -76,7 +75,7 @@ public class PopupMenu extends JPopupMenu catch(Exception e) { e.printStackTrace(); } - SequenceGroup sg = ap.av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); if(sg!=null) { groupName.setText(sg.getName()); @@ -119,30 +118,6 @@ public class PopupMenu extends JPopupMenu private void jbInit() throws Exception { groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copyGroup_actionPerformed(e); - } - }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveGroup_actionPerformed(e); - } - }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSequences_actionPerformed(e); - } - }); analyze.setText("Analyze"); analyze.addActionListener(new java.awt.event.ActionListener() { @@ -160,6 +135,7 @@ public class PopupMenu extends JPopupMenu groupName_actionPerformed(e); } }); + groupAnnotation.setEnabled(false); groupAnnotation.setText("Annotation"); groupAnnotation.addActionListener(new java.awt.event.ActionListener() { @@ -178,6 +154,8 @@ public class PopupMenu extends JPopupMenu } }); residueMenu.setText("Residue"); + annotateResidue.setEnabled(false); + annotateResidue.setActionCommand("annotate residue"); annotateResidue.setText("annotate residue???"); PIDColour.setFocusPainted(false); unGroupMenuItem.setText("Remove Group"); @@ -196,20 +174,26 @@ public class PopupMenu extends JPopupMenu pdbMenuItem_actionPerformed(e); } }); + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(e); + } + }); add(groupMenu); this.add(sequenceMenu); this.add(residueMenu); groupMenu.add(defineMenu); groupMenu.add(unGroupMenuItem); groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); - groupMenu.addSeparator(); groupMenu.add(analyze); defineMenu.add(groupName); defineMenu.add(groupAnnotation); defineMenu.addSeparator(); + defineMenu.add(outline); + defineMenu.addSeparator(); defineMenu.add(noColourmenuItem); defineMenu.add(clustalColour); defineMenu.add(zappoColour); @@ -355,7 +339,6 @@ public class PopupMenu extends JPopupMenu if( superG !=null) superG.setSuperGroupProperties( sg ); - ap.seqPanel.seqCanvas.paintFlag=true; ap.seqPanel.repaint(); } @@ -412,7 +395,29 @@ public class PopupMenu extends JPopupMenu protected void abovePIDColour_actionPerformed(ActionEvent e) { - Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName()); + SequenceGroup sg = getGroup(); + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); + if (sg.cs instanceof ResidueColourScheme) + ( (ResidueColourScheme)sg. cs).setThreshold(threshold); + else if (sg.cs instanceof ScoreColourScheme) + ( (ScoreColourScheme) sg.cs).setThreshold(threshold); + + SliderPanel.showPIDSlider(); + + } + else // remove PIDColouring + { + ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; + rcs.setThreshold(0); + sg.cs = rcs; + } + + refresh(); + } @@ -435,7 +440,7 @@ public class PopupMenu extends JPopupMenu protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - getGroup().cs = new Blosum62ColourScheme(ap.av); + getGroup().cs = new Blosum62ColourScheme(); refresh(); } @@ -459,13 +464,14 @@ public class PopupMenu extends JPopupMenu ap.av.alignment.getWidth()); c.calculate(); - c.verdict(false, 100); + c.verdict(false, ap.av.ConsPercGaps); ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); sg.cs = ccs; - Desktop.setConservationSliderSource(ap, ccs, sg.getName()); + SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.showConservationSlider(); } else // remove ConservationColouring { @@ -492,60 +498,6 @@ public class PopupMenu extends JPopupMenu groupName.setText(reply); } - protected void copyGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - for (int i=0; i < sg.sequences.size(); i++) - { - s[i] = new Sequence( sg.getSequenceAt(i)); - s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) ); - } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if (newHeight > 500) - newHeight = 500; - Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); - } - - protected void moveGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - - for (int i=0; i < sg.sequences.size(); i++) - s[i] = new Sequence( sg.getSequenceAt(i)); - - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if(newHeight>500) - newHeight=500; - Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight); - - - for (int i=0; i < sg.sequences.size(); i++) - ap.av.alignment.deleteSequence(sg.getSequenceAt(i)); - - - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.RefreshPanels(); - - - } - - protected void deleteSequences_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i)); - - ap.av.alignment.deleteGroup(sg); - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.RefreshPanels(); - - } protected void analyze_actionPerformed(ActionEvent e) { @@ -571,10 +523,11 @@ public class PopupMenu extends JPopupMenu SequenceGroup getGroup() { - SequenceGroup sg = ap.av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); // this method won't add a new group if it already exists ap.av.alignment.addGroup(sg); + return sg; } @@ -593,17 +546,17 @@ public class PopupMenu extends JPopupMenu if(s!=null) { sequence.setName(s); - ap.RefreshPanels(); + ap.repaint(); } } void unGroupMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = ap.av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.alignment.deleteGroup(sg); - ap.av.setRubberbandGroup(null); - ap.RefreshPanels(); + ap.av.setSelectionGroup(null); + ap.repaint(); } void pdbMenuItem_actionPerformed(ActionEvent e) @@ -634,4 +587,12 @@ public class PopupMenu extends JPopupMenu } } + protected void outline_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE); + if(col!=null) + sg.setOutlineColour(col); + } + }