X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=c71818e2dae8ab46be141ffdf76a1507b99a0e2a;hb=a90a2ca70e84c2923c682512a27e93785ad65557;hp=300eb940327447f6586155e094d91a0716a4a097;hpb=f13833b55dc6e05e5630b8dc465059a5cd2848a8;p=jalview.git
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 300eb94..c71818e 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,889 +1,1088 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-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();
- 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();
- 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(sg.getName());
- 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);
- }
-
- 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 == 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 == 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(),
- 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 gSize = sg.getSize();
- SequenceI[] seqs = new SequenceI[gSize];
- SequenceFeature[] features = new SequenceFeature[gSize];
-
- for (int i = 0; i < gSize; i++)
- {
- seqs[i] = sg.getSequenceAt(i);
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
- int end = sg.findEndRes(sg.getSequenceAt(i));
- features[i] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
- }
-
- 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 ", 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);
-
- 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");
- menu1.setLabel("Group");
- add(groupMenu);
- this.add(seqMenu);
- this.add(hideSeqs);
- 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);
- 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);
- }
-
- 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 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);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 Annotation for " + seq.getDisplayId(true)
+ + "
"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("
"); + } + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 600, 500); + cap.setText("" + contents.toString() + ""); + } + + 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); + sequenceDetails.addActionListener(this); + selSeqDetails.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(selSeqDetails); + 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); + // seqMenu.add(sequenceDetails); + + 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, ap.av.getHiddenRepSequences()); + 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 + .getHiddenRepSequences()), 0, ap.av.getAlignment().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 + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); + refresh(); + } + + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().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()) + { + + sg.cs.setConservation(Conservation.calculateConservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment() + .getWidth(), false, ap.av.getConsPercGaps(), false)); + 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.getAlignment().addGroup(sg); + } + + return sg; + } + + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.getAlignment().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(); + } + +}