X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=35fe48b0f57f6b3def781897fa03ef6d86f2216b;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=858770a35ec187ca5849712d7b189fa046e988c6;hpb=29f89f52f3fc99e904a55e426c53a830290408cc;p=jalview.git
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 858770a..35fe48b 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,531 +1,1089 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
-{
- 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();
-
- 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();
-
- public APopupMenu(AlignmentPanel ap, 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 = ap;
-
- try
- {
- jbInit();
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
-
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg != null)
- {
- showText.setState(sg.getDisplayText());
- showColourText.setState(sg.getColourText());
- showBoxes.setState(sg.getDisplayBoxes());
- }
-
- if (!ap.av.alignment.getGroups().contains(sg))
- {
- groupMenu.remove(unGroupMenuItem);
- }
-
- if (seq != null && links!=null)
- {
- Menu linkMenu = new Menu("Link");
- MenuItem item;
- String link;
- for(int i=0; i.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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;
+import jalview.io.SequenceAnnotationReport;
+
+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");
+
+ MenuItem sequenceDetails = new MenuItem("Sequence Details ...");
+
+ MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
+
+ 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.getAlignment().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 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.getAlignment().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 == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
+ 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.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+
+ 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[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ 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.getHiddenRepSequences()),
+ 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);
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
+ // now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
+
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+ e.getActionCommand(),
+ new Alignment(ap.av.getSelectionAsNewSequence()),
+ ap.av.showJVSuffix));
+
+ }
+
+ protected void showSequenceSelectionDetails()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void showSequenceDetails()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { seq });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append("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();
+ }
+
+}