-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class APopupMenu extends java.awt.PopupMenu\r
-{\r
- Menu groupMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
-\r
-\r
- AlignmentPanel ap;\r
- Menu sequenceMenu = new Menu();\r
- MenuItem sequenceName = new MenuItem();\r
- Sequence sequence;\r
- MenuItem unGroupMenuItem = new MenuItem();\r
- MenuItem nucleotideMenuItem = new MenuItem();\r
-\r
- public APopupMenu(AlignmentPanel ap, Sequence seq)\r
- {\r
- ///////////////////////////////////////////////////////////\r
- // If this is activated from the sequence panel, the user may want to\r
- // edit or annotate a particular residue. Therefore display the residue menu\r
- //\r
- // If from the IDPanel, we must display the sequence menu\r
- //////////////////////////////////////////////////////////\r
-\r
- this.ap = ap;\r
- sequence = seq;\r
-\r
- try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
-\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
- groupMenu.remove(unGroupMenuItem);\r
-\r
- if(seq==null)\r
- remove(sequenceMenu);\r
-\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Define");\r
-\r
- sequenceMenu.setLabel("Sequence");\r
- sequenceName.setLabel("Edit name");\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- conservationMenuItem_itemStateChanged(itemEvent);\r
- }\r
- });\r
- abovePIDColour.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- abovePIDColour_itemStateChanged(itemEvent);\r
- }\r
- });\r
-\r
- add(groupMenu);\r
- this.add(sequenceMenu);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(noColourmenuItem);\r
- groupMenu.add(clustalColour);\r
- groupMenu.add(BLOSUM62Colour);\r
- groupMenu.add(PIDColour);\r
-\r
- groupMenu.add(zappoColour);\r
- groupMenu.add(taylorColour);\r
- groupMenu.add(hydrophobicityColour);\r
- groupMenu.add(helixColour);\r
- groupMenu.add(strandColour);\r
- groupMenu.add(turnColour);\r
- groupMenu.add(buriedColour);\r
- groupMenu.add(nucleotideMenuItem);\r
-\r
- groupMenu.add(userDefinedColour);\r
-\r
- groupMenu.addSeparator();\r
- groupMenu.add(abovePIDColour);\r
- groupMenu.add(conservationMenuItem);\r
-\r
- sequenceMenu.add(sequenceName);\r
-\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
- clustalColour.setLabel("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setLabel("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setLabel("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setLabel("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- abovePIDColour.setLabel("Above % Identity");\r
-\r
- userDefinedColour.setLabel("User Defined");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setLabel("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setLabel("Conservation");\r
-\r
-\r
- }\r
-\r
- void refresh()\r
- {\r
- SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
-\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
-\r
- protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (abovePIDColour.getState())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-\r
- SliderPanel.showPIDSlider();\r
-\r
-\r
- }\r
- else // remove PIDColouring\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
- }\r
-\r
- refresh();\r
-\r
- }\r
-\r
-\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
- }\r
-\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
-\r
- refresh();\r
- }\r
-\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if(conservationMenuItem.getState())\r
- {\r
-\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
-\r
- sg.cs = ccs;\r
-\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
-\r
- refresh();\r
- }\r
-\r
-\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.elementAt(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
-\r
- }\r
-\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- // this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\r
-\r
- return sg;\r
- }\r
-\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class APopupMenu
+ extends java.awt.PopupMenu implements ActionListener, ItemListener
+{
+ Menu groupMenu = new Menu();
+ protected MenuItem clustalColour = new MenuItem();
+ protected MenuItem zappoColour = new MenuItem();
+ protected MenuItem taylorColour = new MenuItem();
+ protected MenuItem hydrophobicityColour = new MenuItem();
+ protected MenuItem helixColour = new MenuItem();
+ protected MenuItem strandColour = new MenuItem();
+ protected MenuItem turnColour = new MenuItem();
+ protected MenuItem buriedColour = new MenuItem();
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ protected MenuItem userDefinedColour = new MenuItem();
+ protected MenuItem PIDColour = new MenuItem();
+ protected MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem noColourmenuItem = new MenuItem();
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ final AlignmentPanel ap;
+ MenuItem unGroupMenuItem = new MenuItem();
+ MenuItem nucleotideMenuItem = new MenuItem();
+ Menu colourMenu = new Menu();
+ CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+ CheckboxMenuItem showText = new CheckboxMenuItem();
+ CheckboxMenuItem showColourText = new CheckboxMenuItem();
+ Menu editMenu = new Menu("Edit");
+ MenuItem copy = new MenuItem("Copy (Jalview Only)");
+ MenuItem cut = new MenuItem("Cut (Jalview Only)");
+ MenuItem toUpper = new MenuItem("To Upper Case");
+ MenuItem toLower = new MenuItem("To Lower Case");
+ MenuItem toggleCase = new MenuItem("Toggle Case");
+ Menu outputmenu = new Menu();
+ Menu seqMenu = new Menu();
+ MenuItem pdb = new MenuItem();
+ MenuItem hideSeqs = new MenuItem();
+ MenuItem repGroup = new MenuItem();
+
+ Sequence seq;
+ MenuItem revealAll = new MenuItem();
+
+ public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
+ {
+ ///////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ //////////////////////////////////////////////////////////
+
+ this.ap = apanel;
+ this.seq = seq;
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
+
+ item.addActionListener(this);
+ outputmenu.add(item);
+ }
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null && sg.getSize(false)>0)
+ {
+ showText.setState(sg.getDisplayText());
+ showColourText.setState(sg.getColourText());
+ showBoxes.setState(sg.getDisplayBoxes());
+ if (!ap.av.alignment.getGroups().contains(sg))
+ {
+ groupMenu.remove(unGroupMenuItem);
+ }
+
+ }
+ else
+ {
+ remove(hideSeqs);
+ remove(groupMenu);
+ }
+
+ if (links!=null)
+ {
+ Menu linkMenu = new Menu("Link");
+ MenuItem item;
+ String link;
+ for(int i=0; i<links.size(); i++)
+ {
+ link = links.elementAt(i).toString();
+ final String target = link.substring(0, link.indexOf("|"));
+ item = new MenuItem(target);
+
+ final String url;
+
+ if (link.indexOf("$SEQUENCE_ID$") > -1)
+ {
+ String id = seq.getName();
+ if (id.indexOf("|") > -1)
+ id = id.substring(id.lastIndexOf("|") + 1);
+
+ url = link.substring(link.indexOf("|") + 1,
+ link.indexOf("$SEQUENCE_ID$"))
+ + id +
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ }
+ 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)
+ {
+ ap.alignFrame.showURL(url, target);
+ }
+ });
+ linkMenu.add(item);
+ }
+ if(seq!=null)
+ seqMenu.add(linkMenu);
+ else
+ add(linkMenu);
+ }
+ if(seq!=null)
+ {
+ seqMenu.setLabel(seq.getName());
+ repGroup.setLabel("Represent Group with " + seq.getName());
+ }
+ else
+ remove(seqMenu);
+
+ if(!ap.av.hasHiddenRows)
+ remove(revealAll);
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if(evt.getSource()==abovePIDColour)
+ abovePIDColour_itemStateChanged();
+ else if(evt.getSource()==showColourText)
+ showColourText_itemStateChanged();
+ else if(evt.getSource()==showText)
+ showText_itemStateChanged();
+ else if(evt.getSource()==showBoxes)
+ showBoxes_itemStateChanged() ;
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+ if(source==clustalColour)
+ clustalColour_actionPerformed();
+ else if(source==zappoColour)
+ zappoColour_actionPerformed();
+ else if(source==taylorColour)
+ taylorColour_actionPerformed();
+ else if(source==hydrophobicityColour)
+ hydrophobicityColour_actionPerformed();
+ else if(source==helixColour)
+ helixColour_actionPerformed();
+ else if(source==strandColour)
+ strandColour_actionPerformed();
+ else if(source==clustalColour)
+ turnColour_actionPerformed();
+ else if(source==buriedColour)
+ buriedColour_actionPerformed();
+ else if(source==nucleotideMenuItem)
+ nucleotideMenuItem_actionPerformed();
+
+ else if (source == userDefinedColour)
+ userDefinedColour_actionPerformed();
+ else if (source == PIDColour)
+ PIDColour_actionPerformed();
+ else if (source == BLOSUM62Colour)
+ BLOSUM62Colour_actionPerformed();
+ else if (source == noColourmenuItem)
+ noColourmenuItem_actionPerformed();
+ else if (source == conservationMenuItem)
+ conservationMenuItem_itemStateChanged();
+ else if (source == unGroupMenuItem)
+ unGroupMenuItem_actionPerformed();
+
+ else if(source == pdb)
+ addPDB();
+ else if(source == hideSeqs)
+ hideSequences(false);
+ else if(source == repGroup)
+ hideSequences(true);
+ else if(source == revealAll)
+ {
+ ap.av.showAllHiddenSeqs();
+ }
+
+ else if(source==copy)
+ ap.alignFrame.copy_actionPerformed();
+ else if(source==cut)
+ ap.alignFrame.cut_actionPerformed();
+ else if(source==toUpper || source==toLower || source==toggleCase)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
+ {
+ for (int g = 0; g < sg.getSize(true); g++)
+ {
+ 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());
+ }
+ ap.seqPanel.seqCanvas.repaint();
+ }
+ }
+ else
+ outputText(evt);
+
+ }
+
+ 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 );
+ }
+ }
+
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Selection output - " + e.getActionCommand(),
+ 600, 500);
+
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+ e.getActionCommand(),
+ vseqs,
+ ap.av.showJVSuffix));
+
+ }
+
+ void addPDB()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+ cap.setText("Paste your PDB file here.");
+ cap.setPDBImport(seq);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ groupMenu.setLabel("Group");
+ groupMenu.setLabel("Selection");
+
+ unGroupMenuItem.setLabel("Remove Group");
+ unGroupMenuItem.addActionListener(this);
+
+ nucleotideMenuItem.setLabel("Nucleotide");
+ nucleotideMenuItem.addActionListener(this);
+ conservationMenuItem.addItemListener(this);
+ abovePIDColour.addItemListener(this);
+ colourMenu.setLabel("Group Colour");
+ showBoxes.setLabel("Boxes");
+ showBoxes.setState(true);
+ showBoxes.addItemListener(this);
+
+ showText.setLabel("Text");
+ showText.addItemListener(this);
+ showColourText.setLabel("Colour Text");
+ showColourText.addItemListener(this);
+ outputmenu.setLabel("Output to Textbox...");
+ seqMenu.setLabel("Sequence");
+ pdb.setLabel("View PDB Structure");
+ hideSeqs.setLabel("Hide Sequences");
+ repGroup.setLabel("Represent Group with");
+ revealAll.setLabel("Reveal All");
+
+ 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);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+
+ noColourmenuItem.setLabel("None");
+ noColourmenuItem.addActionListener(this);
+
+ clustalColour.setLabel("Clustalx colours");
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel("Zappo");
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel("Taylor");
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.addActionListener(this);
+ helixColour.setLabel("Helix propensity");
+ helixColour.addActionListener(this);
+ strandColour.setLabel("Strand propensity");
+ strandColour.addActionListener(this);
+ turnColour.setLabel("Turn propensity");
+ turnColour.addActionListener(this);
+ buriedColour.setLabel("Buried Index");
+ buriedColour.addActionListener(this);
+ abovePIDColour.setLabel("Above % Identity");
+
+ userDefinedColour.setLabel("User Defined");
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel("Percentage Identity");
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel("BLOSUM62");
+ BLOSUM62Colour.addActionListener(this);
+ conservationMenuItem.setLabel("Conservation");
+
+ editMenu.add(copy);
+ copy.addActionListener(this);
+ editMenu.add(cut);
+ cut.addActionListener(this);
+ editMenu.add(toUpper);
+ toUpper.addActionListener(this);
+ editMenu.add(toLower);
+ toLower.addActionListener(this);
+ editMenu.add(toggleCase);
+ seqMenu.add(pdb);
+ seqMenu.add(repGroup);
+ toggleCase.addActionListener(this);
+ pdb.addActionListener(this);
+ hideSeqs.addActionListener(this);
+ repGroup.addActionListener(this);
+ revealAll.addActionListener(this);
+
+ }
+
+ void refresh()
+ {
+ ap.seqPanel.seqCanvas.repaint();
+ if(ap.overviewPanel!=null)
+ ap.overviewPanel.updateOverviewImage();
+ }
+
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
+ refresh();
+ }
+
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ZappoColourScheme();
+ refresh();
+ }
+
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new TaylorColourScheme();
+ refresh();
+ }
+
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new HydrophobicColourScheme();
+ refresh();
+ }
+
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new HelixColourScheme();
+ refresh();
+ }
+
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new StrandColourScheme();
+ refresh();
+ }
+
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new TurnColourScheme();
+ refresh();
+ }
+
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new BuriedColourScheme();
+ refresh();
+ }
+
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new NucleotideColourScheme();
+ refresh();
+ }
+
+ protected void abovePIDColour_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if(sg.cs==null)
+ return;
+
+ if (abovePIDColour.getState())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+
+ }
+ else // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ }
+
+ refresh();
+
+ }
+
+ protected void userDefinedColour_actionPerformed()
+ {
+ new UserDefinedColours(ap, getGroup());
+ }
+
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+ refresh();
+ }
+
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+
+ refresh();
+ }
+
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ protected void conservationMenuItem_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if(sg.cs==null)
+ return;
+
+ if (conservationMenuItem.getState())
+ {
+
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(true), 0,
+ ap.av.alignment.getWidth());
+
+ c.calculate();
+ c.verdict(false, ap.av.ConsPercGaps);
+
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ // this method won't add a new group if it already exists
+ if(sg!=null)
+ ap.av.alignment.addGroup(sg);
+
+ return sg;
+ }
+
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.alignment.deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ ap.repaint();
+ }
+
+ public void showColourText_itemStateChanged()
+ {
+ getGroup().setColourText(showColourText.getState());
+ refresh();
+ }
+
+ public void showText_itemStateChanged()
+ {
+ getGroup().setDisplayText(showText.getState());
+ refresh();
+ }
+
+ public void showBoxes_itemStateChanged()
+ {
+ getGroup().setDisplayBoxes(showBoxes.getState());
+ refresh();
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if(sg==null || sg.getSize(false)<1)
+ {
+ ap.av.hideSequence(seq);
+ return;
+ }
+
+ int index = 0;
+ while(index < sg.getSize(false))
+ {
+ if(representGroup && sg.getSequenceAt(index)!=seq)
+ {
+ seq.addHiddenSequence(sg.getSequenceAt(index));
+ ap.av.hideSequence(sg.getSequenceAt(index));
+ }
+ else if(!representGroup)
+ {
+ ap.av.hideSequence(sg.getSequenceAt(index));
+ }
+ index ++;
+ }
+
+ ap.av.setSelectionGroup(null);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff