-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.util.Vector;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class APopupMenu\r
- extends java.awt.PopupMenu implements ActionListener, ItemListener\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
- final AlignmentPanel ap;\r
- MenuItem unGroupMenuItem = new MenuItem();\r
- MenuItem nucleotideMenuItem = new MenuItem();\r
- Menu colourMenu = new Menu();\r
- CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
- CheckboxMenuItem showText = new CheckboxMenuItem();\r
- CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
- Menu editMenu = new Menu("Edit");\r
- MenuItem copy = new MenuItem("Copy (Jalview Only)");\r
- MenuItem cut = new MenuItem("Cut (Jalview Only)");\r
- MenuItem toUpper = new MenuItem("To Upper Case");\r
- MenuItem toLower = new MenuItem("To Lower Case");\r
- MenuItem toggleCase = new MenuItem("Toggle Case");\r
- Menu outputmenu = new Menu();\r
- Menu seqMenu = new Menu();\r
- MenuItem pdb = new MenuItem();\r
- MenuItem hideSeqs = new MenuItem();\r
- MenuItem repGroup = new MenuItem();\r
-\r
- Sequence seq;\r
- MenuItem revealAll = new MenuItem();\r
-\r
- public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\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 = apanel;\r
- this.seq = seq;\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
-\r
- item.addActionListener(this);\r
- outputmenu.add(item);\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null && sg.getSize(false)>0)\r
- {\r
- showText.setState(sg.getDisplayText());\r
- showColourText.setState(sg.getColourText());\r
- showBoxes.setState(sg.getDisplayBoxes());\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- groupMenu.remove(unGroupMenuItem);\r
- }\r
-\r
- }\r
- else\r
- {\r
- remove(hideSeqs);\r
- remove(groupMenu);\r
- }\r
-\r
- if (links!=null)\r
- {\r
- Menu linkMenu = new Menu("Link");\r
- MenuItem item;\r
- String link;\r
- for(int i=0; i<links.size(); i++)\r
- {\r
- link = links.elementAt(i).toString();\r
- final String target = link.substring(0, link.indexOf("|"));\r
- item = new MenuItem(target);\r
-\r
- final String url;\r
-\r
- if (link.indexOf("$SEQUENCE_ID$") > -1)\r
- {\r
- String id = seq.getName();\r
- if (id.indexOf("|") > -1)\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
-\r
- url = link.substring(link.indexOf("|") + 1,\r
- link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
- }\r
- else\r
- url = link.substring(link.lastIndexOf("|")+1);\r
-\r
- System.out.println("add "+url +" "+target);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.alignFrame.showURL(url, target);\r
- }\r
- });\r
- linkMenu.add(item);\r
- }\r
- if(seq!=null)\r
- seqMenu.add(linkMenu);\r
- else\r
- add(linkMenu);\r
- }\r
- if(seq!=null)\r
- {\r
- seqMenu.setLabel(seq.getName());\r
- repGroup.setLabel("Represent Group with " + seq.getName());\r
- }\r
- else\r
- remove(seqMenu);\r
-\r
- if(!ap.av.hasHiddenRows)\r
- remove(revealAll);\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if(evt.getSource()==abovePIDColour)\r
- abovePIDColour_itemStateChanged();\r
- else if(evt.getSource()==showColourText)\r
- showColourText_itemStateChanged();\r
- else if(evt.getSource()==showText)\r
- showText_itemStateChanged();\r
- else if(evt.getSource()==showBoxes)\r
- showBoxes_itemStateChanged() ;\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- Object source = evt.getSource();\r
- if(source==clustalColour)\r
- clustalColour_actionPerformed();\r
- else if(source==zappoColour)\r
- zappoColour_actionPerformed();\r
- else if(source==taylorColour)\r
- taylorColour_actionPerformed();\r
- else if(source==hydrophobicityColour)\r
- hydrophobicityColour_actionPerformed();\r
- else if(source==helixColour)\r
- helixColour_actionPerformed();\r
- else if(source==strandColour)\r
- strandColour_actionPerformed();\r
- else if(source==turnColour)\r
- turnColour_actionPerformed();\r
- else if(source==buriedColour)\r
- buriedColour_actionPerformed();\r
- else if(source==nucleotideMenuItem)\r
- nucleotideMenuItem_actionPerformed();\r
-\r
- else if (source == userDefinedColour)\r
- userDefinedColour_actionPerformed();\r
- else if (source == PIDColour)\r
- PIDColour_actionPerformed();\r
- else if (source == BLOSUM62Colour)\r
- BLOSUM62Colour_actionPerformed();\r
- else if (source == noColourmenuItem)\r
- noColourmenuItem_actionPerformed();\r
- else if (source == conservationMenuItem)\r
- conservationMenuItem_itemStateChanged();\r
- else if (source == unGroupMenuItem)\r
- unGroupMenuItem_actionPerformed();\r
-\r
- else if(source == pdb)\r
- addPDB();\r
- else if(source == hideSeqs)\r
- hideSequences(false);\r
- else if(source == repGroup)\r
- hideSequences(true);\r
- else if(source == revealAll)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- }\r
-\r
- else if(source==copy)\r
- ap.alignFrame.copy_actionPerformed();\r
- else if(source==cut)\r
- ap.alignFrame.cut_actionPerformed();\r
- else if(source==toUpper || source==toLower || source==toggleCase)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null)\r
- {\r
- for (int g = 0; g < sg.getSize(true); g++)\r
- {\r
- int start = sg.getStartRes();\r
- int end = sg.getEndRes() + 1;\r
-\r
- do\r
- {\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- end = ap.av.colSel.getHiddenBoundaryRight(start);\r
- if (start == end)\r
- end = sg.getEndRes() + 1;\r
- if (end > sg.getEndRes())\r
- end = sg.getEndRes() + 1;\r
- }\r
-\r
- if (source == toggleCase)\r
- ( (SequenceI) sg.getSequences(true).elementAt(g))\r
- .toggleCase(start, end);\r
- else\r
- ( (SequenceI) sg.getSequences(true).elementAt(g))\r
- .changeCase(source == toUpper, start, end);\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- start = ap.av.colSel.adjustForHiddenColumns(end);\r
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
- }\r
-\r
- }\r
- while (end < sg.getEndRes());\r
- }\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
- }\r
- else\r
- outputText(evt);\r
-\r
- }\r
-\r
- void outputText(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
- Vector vseqs = new Vector();\r
-\r
- String [] selection = ap.av.getViewAsString(true);\r
- SequenceI [] seqs = ap.av.getSelectionAsNewSequence();\r
- if (selection != null)\r
- {\r
- for (int i = 0; i < selection.length; i++)\r
- {\r
- Sequence seq = new Sequence(\r
- seqs[i].getName(),\r
- selection[i],\r
- seqs[i].getStart(), seqs[i].getEnd());\r
- seq.setDescription(seqs[i].getDescription());\r
- vseqs.addElement( seq );\r
- }\r
- }\r
-\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Selection output - " + e.getActionCommand(),\r
- 600, 500);\r
-\r
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- vseqs,\r
- ap.av.showJVSuffix));\r
-\r
- }\r
-\r
- void addPDB()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
- cap.setText("Paste your PDB file here.");\r
- cap.setPDBImport(seq);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Selection");\r
-\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(this);\r
-\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(this);\r
- conservationMenuItem.addItemListener(this);\r
- abovePIDColour.addItemListener(this);\r
- colourMenu.setLabel("Group Colour");\r
- showBoxes.setLabel("Boxes");\r
- showBoxes.setState(true);\r
- showBoxes.addItemListener(this);\r
-\r
- showText.setLabel("Text");\r
- showText.addItemListener(this);\r
- showColourText.setLabel("Colour Text");\r
- showColourText.addItemListener(this);\r
- outputmenu.setLabel("Output to Textbox...");\r
- seqMenu.setLabel("Sequence");\r
- pdb.setLabel("View PDB Structure");\r
- hideSeqs.setLabel("Hide Sequences");\r
- repGroup.setLabel("Represent Group with");\r
- revealAll.setLabel("Reveal All");\r
-\r
- add(groupMenu);\r
- this.add(seqMenu);\r
- this.add(hideSeqs);\r
- this.add(revealAll);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputmenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideMenuItem);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
-\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(this);\r
-\r
- clustalColour.setLabel("Clustalx colours");\r
- clustalColour.addActionListener(this);\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(this);\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(this);\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(this);\r
- helixColour.setLabel("Helix propensity");\r
- helixColour.addActionListener(this);\r
- strandColour.setLabel("Strand propensity");\r
- strandColour.addActionListener(this);\r
- turnColour.setLabel("Turn propensity");\r
- turnColour.addActionListener(this);\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(this);\r
- abovePIDColour.setLabel("Above % Identity");\r
-\r
- userDefinedColour.setLabel("User Defined");\r
- userDefinedColour.addActionListener(this);\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(this);\r
- BLOSUM62Colour.setLabel("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(this);\r
- conservationMenuItem.setLabel("Conservation");\r
-\r
- editMenu.add(copy);\r
- copy.addActionListener(this);\r
- editMenu.add(cut);\r
- cut.addActionListener(this);\r
- editMenu.add(toUpper);\r
- toUpper.addActionListener(this);\r
- editMenu.add(toLower);\r
- toLower.addActionListener(this);\r
- editMenu.add(toggleCase);\r
- seqMenu.add(pdb);\r
- seqMenu.add(repGroup);\r
- toggleCase.addActionListener(this);\r
- pdb.addActionListener(this);\r
- hideSeqs.addActionListener(this);\r
- repGroup.addActionListener(this);\r
- revealAll.addActionListener(this);\r
-\r
- }\r
-\r
- void refresh()\r
- {\r
- ap.seqPanel.seqCanvas.repaint();\r
- if(ap.overviewPanel!=null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
-\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void abovePIDColour_itemStateChanged()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
-\r
- if (abovePIDColour.getState())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
-\r
- }\r
- else // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
-\r
- }\r
-\r
- protected void userDefinedColour_actionPerformed()\r
- {\r
- new UserDefinedColours(ap, getGroup());\r
- }\r
-\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
- refresh();\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
-\r
- refresh();\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- protected void conservationMenuItem_itemStateChanged()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
-\r
- if (conservationMenuItem.getState())\r
- {\r
-\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\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
- if(sg!=null)\r
- ap.av.alignment.addGroup(sg);\r
-\r
- return sg;\r
- }\r
-\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- }\r
-\r
- public void showColourText_itemStateChanged()\r
- {\r
- getGroup().setColourText(showColourText.getState());\r
- refresh();\r
- }\r
-\r
- public void showText_itemStateChanged()\r
- {\r
- getGroup().setDisplayText(showText.getState());\r
- refresh();\r
- }\r
-\r
- public void showBoxes_itemStateChanged()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.getState());\r
- refresh();\r
- }\r
-\r
- void hideSequences(boolean representGroup)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize(false)<1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]{seq});\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize(false);\r
- SequenceI [] hseqs;\r
-\r
- hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
-\r
- int index = 0;\r
- for(int i=0; i<gsize; i++)\r
- {\r
- if(representGroup && sg.getSequenceAt(i)!=seq)\r
- {\r
- seq.addHiddenSequence(sg.getSequenceAt(i));\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
- else if(!representGroup)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
- }\r
-\r
- ap.av.hideSequence(hseqs);\r
-\r
- ap.av.setSelectionGroup(null);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.UrlLink;
+import jalview.io.AppletFormatAdapter;
+
+public class APopupMenu extends java.awt.PopupMenu implements
+ ActionListener, ItemListener
+{
+ Menu groupMenu = new Menu();
+
+ MenuItem editGroupName = new MenuItem();
+
+ 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();
+
+ CheckboxMenuItem displayNonconserved = 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();
+
+ MenuItem sequenceName = new MenuItem("Edit Name/Description");
+
+ MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+
+ MenuItem editSequence = new MenuItem("Edit Sequence");
+
+ Sequence seq;
+
+ MenuItem revealAll = new MenuItem();
+
+ MenuItem revealSeq = new MenuItem();
+ /**
+ * index of sequence to be revealed
+ */
+ int revealSeq_index=-1;
+ Menu menu1 = new Menu();
+
+ 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() > 0)
+ {
+ editGroupName.setLabel("Name: "+sg.getName());
+ showText.setState(sg.getDisplayText());
+ showColourText.setState(sg.getColourText());
+ showBoxes.setState(sg.getDisplayBoxes());
+ displayNonconserved.setState(sg.getShowNonconserved());
+ if (!ap.av.alignment.getGroups().contains(sg))
+ {
+ groupMenu.remove(unGroupMenuItem);
+ }
+
+ }
+ else
+ {
+ remove(hideSeqs);
+ remove(groupMenu);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+ Menu linkMenu = new Menu("Link");
+ String link;
+ for (int i = 0; i < links.size(); i++)
+ {
+ link = links.elementAt(i).toString();
+ UrlLink urlLink = new UrlLink(link);
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String target = urlLink.getTarget(); // link.substring(0,
+ // link.indexOf("|"));
+ final String label = urlLink.getLabel();
+ if (seq!=null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { target });
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ if (id != null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);
+ }
+ // Now construct URLs from description but only try to do it for regex
+ // URL links
+ if (descr != null && urlLink.getRegexReplace() != null)
+ {
+ // create link for this URL from description only if regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ else
+ {
+ addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+ }
+ /*
+ * final String url;
+ *
+ * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
+ * string and any matching database reference accessions String url_pref
+ * = link.substring(link.indexOf("|") + 1,
+ * link.indexOf("$SEQUENCE_ID$"));
+ *
+ * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ * // collect matching db-refs DBRefEntry[] dbr =
+ * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
+ * String[]{target}); // collect id string too String id =
+ * seq.getName(); if (id.indexOf("|") > -1) { id =
+ * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
+ * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
+ * suppress duplicate link creation for the bare sequence ID string with
+ * this link id = null; } addshowLink(linkMenu,
+ * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
+ * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
+ * create Bare ID link for this RUL addshowLink(linkMenu, target,
+ * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
+ * link.substring(link.lastIndexOf("|")+1)); }
+ */
+ }
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+ // TODO: add group link menu entry here
+ if (seq != null)
+ {
+ seqMenu.setLabel(seq.getName());
+ repGroup.setLabel("Represent Group with " + seq.getName());
+ }
+ else
+ {
+ remove(seqMenu);
+ }
+
+ if (!ap.av.hasHiddenRows)
+ {
+ remove(revealAll);
+ remove(revealSeq);
+ } else {
+ final int index = ap.av.alignment.findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ revealSeq_index=index;
+ } else {
+ remove(revealSeq);
+ }
+ }
+ }
+
+ /**
+ * add a show URL menu item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param target
+ * - menu label string
+ * @param url
+ * - url to open
+ */
+ private void addshowLink(Menu linkMenu, final String target,
+ final String url)
+ {
+ addshowLink(linkMenu, target, target, url);
+ }
+
+ /**
+ * add a show URL menu item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param target
+ * - URL target window
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
+ */
+ private void addshowLink(Menu linkMenu, final String target,
+ final String label, final String url)
+ {
+ MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.showURL(url, target);
+ }
+ });
+ linkMenu.add(item);
+ }
+
+ 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();
+ }
+ else if (evt.getSource() == displayNonconserved)
+ {
+ this.showNonconserved_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 == turnColour)
+ {
+ 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 == sequenceName)
+ {
+ editName();
+ }
+ else if (source == pdb)
+ {
+ addPDB();
+ }
+ else if (source == hideSeqs)
+ {
+ hideSequences(false);
+ }
+ else if (source == repGroup)
+ {
+ hideSequences(true);
+ }
+ else if (source == revealSeq)
+ {
+ ap.av.showSequence(revealSeq_index);
+ }
+ else if (source == revealAll)
+ {
+ ap.av.showAllHiddenSeqs();
+ }
+
+ else if (source == editGroupName)
+ {
+ EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+ getGroup().getDescription(), " Group Name",
+ "Group Description", ap.alignFrame,
+ "Edit Group Name / Description", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ getGroup().setName(dialog.getName().replace(' ', '_'));
+ getGroup().setDescription(dialog.getDescription());
+ }
+
+ }
+ else if (source == copy)
+ {
+ ap.alignFrame.copy_actionPerformed();
+ }
+ else if (source == cut)
+ {
+ ap.alignFrame.cut_actionPerformed();
+ }
+ else if (source == editSequence)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ if (seq == null)
+ seq = (Sequence) sg.getSequenceAt(0);
+
+ EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
+ sg.getStartRes(), sg.getEndRes() + 1), null,
+ "Edit Sequence ", null,
+
+ ap.alignFrame, "Edit Sequence", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ 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);
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+ }
+ }
+ }
+ else if (source == toUpper || source == toLower || source == toggleCase)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ Vector regions = new Vector();
+ if (sg != null)
+ {
+ int start = sg.getStartRes();
+ int end = sg.getEndRes() + 1;
+
+ do
+ {
+ 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)
+ {
+ start = ap.av.colSel.adjustForHiddenColumns(end);
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ } 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 if (source == sequenceFeature)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
+ for (int i = 0; i < gSize; i++)
+ {
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+ int end = sg.findEndRes(sg.getSequenceAt(i));
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i);
+ features[rsize] = new SequenceFeature(null, null, null, start,
+ end, "Jalview");
+ rsize++;
+ }
+ }
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ ap.av.showSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+ else
+ {
+ outputText(evt);
+ }
+
+ }
+
+ void outputText(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+ 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(),
+ new Alignment(ap.av.getSelectionAsNewSequence()),
+ ap.av.showJVSuffix));
+
+ }
+
+ void editName()
+ {
+ EditNameDialog dialog = new EditNameDialog(seq.getName(),
+ seq.getDescription(), " Sequence Name",
+ "Sequence Description", ap.alignFrame,
+ "Edit Sequence Name / Description", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ seq.setName(dialog.getName());
+ seq.setDescription(dialog.getDescription());
+ ap.paintAlignment(false);
+ }
+ }
+
+ void addPDB()
+ {
+ if (seq.getPDBId() != null)
+ {
+ PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
+
+ if (ap.av.applet.jmolAvailable)
+ new jalview.appletgui.AppletJmol(entry, new Sequence[]
+ { seq }, null, ap, AppletFormatAdapter.URL);
+ else
+ new MCview.AppletPDBViewer(entry, new Sequence[]
+ { seq }, null, ap, AppletFormatAdapter.URL);
+
+ }
+ else
+ {
+ 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 for sequence "+seq.getName(), 400, 300);
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ groupMenu.setLabel("Group");
+ groupMenu.setLabel("Selection");
+ sequenceFeature.addActionListener(this);
+
+ editGroupName.addActionListener(this);
+ 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);
+ sequenceName.addActionListener(this);
+ displayNonconserved.setLabel("Show Nonconserved");
+ displayNonconserved.setState(false);
+ displayNonconserved.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");
+ revealSeq.setLabel("Reveal Sequences");
+ menu1.setLabel("Group");
+ add(groupMenu);
+ this.add(seqMenu);
+ this.add(hideSeqs);
+ this.add(revealSeq);
+ this.add(revealAll);
+ groupMenu.add(editGroupName);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputmenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(menu1);
+
+ 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(editSequence);
+ editSequence.addActionListener(this);
+
+ editMenu.add(toUpper);
+ toUpper.addActionListener(this);
+ editMenu.add(toLower);
+ toLower.addActionListener(this);
+ editMenu.add(toggleCase);
+ seqMenu.add(sequenceName);
+ if (!ap.av.applet.useXtrnalSviewer)
+ {
+ seqMenu.add(pdb);
+ }
+ seqMenu.add(repGroup);
+ menu1.add(unGroupMenuItem);
+ menu1.add(colourMenu);
+ menu1.add(showBoxes);
+ menu1.add(showText);
+ menu1.add(showColourText);
+ menu1.add(displayNonconserved);
+ toggleCase.addActionListener(this);
+ pdb.addActionListener(this);
+ hideSeqs.addActionListener(this);
+ repGroup.addActionListener(this);
+ revealAll.addActionListener(this);
+ revealSeq.addActionListener(this);
+ }
+
+ void refresh()
+ {
+ ap.paintAlignment(true);
+ }
+
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(ap.av.hiddenRepSequences),
+ 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(ap.av.hiddenRepSequences), 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(ap.av.hiddenRepSequences), 0,
+ ap.av.alignment.getWidth()));
+ refresh();
+ }
+
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), 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(ap.av.hiddenRepSequences), 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.paintAlignment(true);
+ }
+
+ public void showColourText_itemStateChanged()
+ {
+ getGroup().setColourText(showColourText.getState());
+ refresh();
+ }
+
+ public void showText_itemStateChanged()
+ {
+ getGroup().setDisplayText(showText.getState());
+ refresh();
+ }
+
+ public void showNonconserved_itemStateChanged()
+ {
+ getGroup().setShowNonconserved(this.displayNonconserved.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() < 1)
+ {
+ ap.av.hideSequence(new SequenceI[]
+ { seq });
+ return;
+ }
+
+ ap.av.setSelectionGroup(null);
+
+ if (representGroup)
+ {
+ ap.av.hideRepSequences(seq, sg);
+
+ return;
+ }
+
+ int gsize = sg.getSize();
+ SequenceI[] hseqs;
+
+ hseqs = new SequenceI[gsize];
+
+ int index = 0;
+ for (int i = 0; i < gsize; i++)
+ {
+ hseqs[index++] = sg.getSequenceAt(i);
+ }
+
+ ap.av.hideSequence(hseqs);
+ ap.av.sendSelection();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff