/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
-import MCview.*;
import jalview.analysis.*;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.*;
import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.UrlLink;
/**
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.118 $
*/
public class PopupMenu extends JPopupMenu
{
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+
+ SequenceI sequence;
JMenuItem unGroupMenuItem = new JMenuItem();
* Creates a new PopupMenu object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
{
this(ap, seq, links, null);
}
+
/**
*
* @param ap
* @param links
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
+ Vector links, Vector groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
colours.add(userDefinedColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
e.printStackTrace();
}
+ JMenuItem menuItem;
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- JMenuItem menuItem;
if (seq.getDatasetSequence().getPDBId() != null
&& seq.getDatasetSequence().getPDBId().size() > 0)
{
{
public void actionPerformed(ActionEvent e)
{
- Vector seqs = new Vector();
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)
- {
- Vector pdbs = ap.av.alignment.getSequenceAt(i)
- .getDatasetSequence().getPDBId();
- if (pdbs == null)
- continue;
-
- for (int p = 0; p < pdbs.size(); p++)
- {
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
- {
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
- seqs.addElement(ap.av.alignment.getSequenceAt(i));
-
- continue;
- }
- }
- }
-
- SequenceI[] seqs2 = new SequenceI[seqs.size()];
- seqs.toArray(seqs2);
-
- new AppJmol(pdb, seqs2, null, ap);
+ // TODO re JAL-860: optionally open dialog or provide a menu entry
+ // allowing user to open just one structure per sequence
+ new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
// new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
}
+
});
viewStructureMenu.add(menuItem);
}
else
{
- structureMenu.remove(viewStructureMenu);
+ if (ap.av.getAlignment().isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
// structureMenu.remove(colStructureMenu);
}
+ if (ap.av.getAlignment().isNucleotide() == true)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ final String rnastruc = aa[i].getRNAStruc();
+ final String structureLine = aa[i].label;
+ menuItem = new JMenuItem();
+ menuItem.setText("2D RNA " + structureLine);
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),
+ rnastruc, seq.getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].getRNAStruc() != null)
+ {
+ final String rnastruc = seqAnno[i].getRNAStruc();
+
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
+ menuItem.setText("2D RNA - " + seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: VARNA does'nt print gaps in the sequence
+ new AppVarna(seq.getName() + " structure", seq, seq
+ .getSequenceAsString(), rnastruc, seq.getName(),
+ ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+ }
+
menuItem = new JMenuItem("Hide Sequences");
menuItem.addActionListener(new java.awt.event.ActionListener()
{
sequenceMenu.add(menuItem);
}
- if (ap.av.hasHiddenRows)
+ if (ap.av.hasHiddenRows())
{
- final int index = ap.av.alignment.findIndex(seq);
+ final int index = ap.av.getAlignment().findIndex(seq);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
});
add(menuItem);
}
-
+ }
+ }
+ // for the case when no sequences are even visible
+ if (ap.av.hasHiddenRows())
+ {
+ {
menuItem = new JMenuItem("Reveal All");
menuItem.addActionListener(new ActionListener()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg != null)
+ if (sg != null && sg.getSize() > 0)
{
- groupName.setText(sg.getName());
+ groupName.setText("Name: " + sg.getName());
+ groupName.setText("Edit name and description of current group.");
if (sg.cs instanceof ZappoColourScheme)
{
{
clustalColour.setSelected(true);
}
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)
+ {
+ purinePyrimidineColour.setSelected(true);
+ }
+ /*
+ * else if (sg.cs instanceof CovariationColourScheme) {
+ * covariationColour.setSelected(true); }
+ */
else
{
noColourmenuItem.setSelected(true);
{
conservationMenuItem.setSelected(true);
}
- displayNonconserved.setSelected(sg.getShowunconserved());
+ displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
showBoxes.setSelected(sg.getDisplayBoxes());
// add any groupURLs to the groupURL submenu and make it visible
- if (groupLinks!=null && groupLinks.size()>0) {
+ if (groupLinks != null && groupLinks.size() > 0)
+ {
buildGroupURLMenu(sg, groupLinks);
}
+ // Add a 'show all structures' for the current selection
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
+ SequenceI sqass = null;
+ for (SequenceI sq : ap.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
+ .getPDBId();
+ if (pes != null)
+ {
+ for (PDBEntry pe : pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ if (pdbe.size() > 0)
+ {
+ final PDBEntry[] pe = pdbe.values().toArray(
+ new PDBEntry[pdbe.size()]);
+ final JMenuItem gpdbview;
+ if (pdbe.size() == 1)
+ {
+ structureMenu.add(gpdbview = new JMenuItem("View structure for "
+ + sqass.getDisplayId(false)));
+ }
+ else
+ {
+ structureMenu.add(gpdbview = new JMenuItem("View all "
+ + pdbe.size() + " structures."));
+ }
+ gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+ gpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ }
+ });
+ }
}
else
{
editMenu.setVisible(false);
}
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
unGroupMenuItem.setVisible(false);
}
if (links != null && links.size() > 0)
{
-
+
JMenu linkMenu = new JMenu("Link");
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
continue;
}
final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
- .getDBRef(), new String[]
- { urlLink.getTarget() });
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
- if (descr!=null && descr.length()<1)
+ if (descr != null && descr.length() < 1)
{
descr = null;
}
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label + "|" + urls[u],
+ urls[u + 1]);
}
}
}
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
}
- // Create urls from description but only for URL links which are regex links
- if (descr != null && urlLink.getRegexReplace()!=null)
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && urlLink.getRegexReplace() != null)
{
// create link for this URL from description where regex matches
String[] urls = urlLink.makeUrls(descr, true);
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
else
{
- if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
{
- linkset.addElement(label+"|"+urlLink.getUrl_prefix());
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
// Add a non-dynamic link
addshowLink(linkMenu, label, urlLink.getUrl_prefix());
}
}
}
}
-
+
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
-
- // TODO: usability: thread off the generation of group url content so root menu appears asap
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
// sequence only URLs
// ID/regex match URLs
groupLinksMenu = new JMenu("Group Link");
- JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
- SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ JMenu[] linkMenus = new JMenu[]
+ { null, new JMenu("IDS"), new JMenu("Sequences"),
+ new JMenu("IDS and Sequences") }; // three types of url that might be
+ // created.
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
- for (int sq = 0; sq<seqs.length;sq++) {
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
- int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
+ .findPosition(sg.getEndRes());
// just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the current selection, too
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence()!=null) {
- sqi = sqi.getDatasetSequence(); }
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr!=null && dbr.length>0)
+ if (dbr != null && dbr.length > 0)
{
- for (int d=0;d<dbr.length;d++)
+ for (int d = 0; d < dbr.length; d++)
{
- String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
Object[] sarray = (Object[]) commonDbrefs.get(src);
- if (sarray==null)
+ if (sarray == null)
{
sarray = new Object[2];
- sarray[0] = new int[] { 0 };
+ sarray[0] = new int[]
+ { 0 };
sarray[1] = new String[seqs.length];
-
- commonDbrefs.put(src,sarray);
+
+ commonDbrefs.put(src, sarray);
}
-
- if (((String[])sarray[1])[sq]==null) {
- if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
- ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
- ((int[])sarray[0])[0]++;
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!dbr[d].hasMap()
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((int[]) sarray[0])[0]++;
}
}
}
}
}
// now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give to user
- for (int i = 0; i < groupLinks.size(); i++) {
- String link = groupLinks.elementAt(i).toString();
- GroupUrlLink urlLink = null;
- try
- {
- urlLink = new GroupUrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- boolean usingNames = false;
- // Now see which parts of the group apply for this URL
- String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- String[] seqstr,ids; // input to makeUrl
- if (idset!=null)
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (int i = 0; i < groupLinks.size(); i++)
+ {
+ String link = groupLinks.elementAt(i).toString();
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
- int numinput = ((int[])idset[0])[0];
- String[] allids = ((String[])idset[1]);
- seqstr = new String[numinput];
- ids = new String[numinput];
- for (int sq=0,idcount=0;sq<seqs.length;sq++)
+ if (allids[sq] != null)
{
- if (allids[sq]!=null) {
- ids[idcount] = allids[sq];
- seqstr[idcount++] = idandseqs[1][sq];
- }
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
}
- } else {
- // just use the id/seq set
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- usingNames=true;
- }
- // and try and make the groupURL!
-
- Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
- if (urlset!=null)
- {
- int type = urlLink.getGroupURLType() & 3;
- //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
- // first two bits ofurlLink type bitfield are sequenceids and sequences
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), urlLink, urlset);
- addMenu = true;
}
}
+ else
+ {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
+ }
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
+ {
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // System.out.println(urlLink.getGroupURLType()
+ // +" "+((String[])urlset[3])[0]);
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type], label
+ + (((type & 1) == 1) ? ("("
+ + (usingNames ? "Names" : ltarget) + ")") : ""),
+ urlLink, urlset);
+ addMenu = true;
+ }
+ }
if (addMenu)
{
groupLinksMenu = new JMenu("Group Links");
- for (int m=0;m<linkMenus.length; m++)
+ for (int m = 0; m < linkMenus.length; m++)
{
- if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
{
groupLinksMenu.add(linkMenus[m]);
}
}
-
+
groupMenu.add(groupLinksMenu);
}
}
* add a show URL menu item to the given linkMenu
*
* @param linkMenu
- * @param label -
- * menu label string
- * @param url -
- * url to open
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
*/
private void addshowLink(JMenu linkMenu, String label, final String url)
{
linkMenu.add(item);
}
+
/**
* add a late bound groupURL item to the given linkMenu
*
* @param linkMenu
- * @param label -
- * menu label string
- * @param urlgenerator GroupURLLink used to generate URL
- * @param urlstub Object array returned from the makeUrlStubs function.
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
*/
- private void addshowLink(JMenu linkMenu, String label, final GroupUrlLink urlgenerator, final Object[] urlstub)
+ private void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL ("+urlgenerator.getUrl_prefix()+"..) ("+urlgenerator.getNumberInvolved(urlstub)+" seqs)"); // TODO: put in info about what is being sent.
+ item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
+ + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
+ // put
+ // in
+ // info
+ // about
+ // what
+ // is
+ // being
+ // sent.
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
public void run()
{
- showLink(urlgenerator.constructFrom(urlstub));
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e)
+ {
+ }
}
}).start();
linkMenu.add(item);
}
+
/**
* DOCUMENT ME!
*
* @throws Exception
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
sequenceName_actionPerformed();
}
});
+ sequenceDetails.setText("Sequence Details ...");
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceDetails_actionPerformed();
+ }
+ });
+ sequenceSelDetails.setText("Sequence Details ...");
+ sequenceSelDetails
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
PIDColour.setFocusPainted(false);
unGroupMenuItem.setText("Remove Group");
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
editSequence_actionPerformed(actionEvent);
}
});
+
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
-
+ groupMenu.add(sequenceSelDetails);
add(groupMenu);
-
add(sequenceMenu);
this.add(structureMenu);
groupMenu.add(editMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
+ if (ap.getAlignment().isNucleotide())
+ {
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
BLOSUM62Colour_actionPerformed();
}
});
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(); } });
+ */
+
conservationMenuItem.setText("Conservation");
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
});
}
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { sequence });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
+ + "</h2></p><p>");
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : null);
+ contents.append("</p>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
+ Desktop.instance.addInternalFrame(cap, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 500, 400);
+
+ }
+
protected void showNonconserved_actionPerformed()
{
- getGroup().setShowunconserved(displayNonconserved.isSelected());
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
- .getWidth());
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void zappoColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void taylorColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void hydrophobicityColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void helixColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void strandColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void turnColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void buriedColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void nucleotideMenuItem_actionPerformed()
{
refresh();
}
+ protected void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void abovePIDColour_actionPerformed()
{
if (abovePIDColour.isSelected())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void userDefinedColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void BLOSUM62Colour_actionPerformed()
{
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed()
{
if (conservationMenuItem.isSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
+ c.verdict(false, ap.av.getConsPercGaps());
sg.cs.setConservation(c);
return;
}
- AnnotationColourGradient acg = new AnnotationColourGradient(sequence
- .getAnnotation()[0], null,
+ AnnotationColourGradient acg = new AnnotationColourGradient(
+ sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
acg.predefinedColours = true;
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void groupName_actionPerformed()
{
SequenceGroup sg = getGroup();
- EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
- .getDescription(), " Group Name ", "Group Description ",
- "Edit Group Name/Description");
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
+ sg.getDescription(), " Group Name ",
+ "Group Description ", "Edit Group Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
}
/**
- * Get selection group - adding it to the alignment if necessary.
+ * Get selection group - adding it to the alignment if necessary.
*
* @return sequence group to operate on
*/
// this method won't add a new group if it already exists
if (sg != null)
{
- ap.av.alignment.addGroup(sg);
+ ap.av.getAlignment().addGroup(sg);
}
return sg;
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void sequenceName_actionPerformed()
{
- EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
- .getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description");
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(), " Sequence Name ",
+ "Sequence Description ", "Edit Sequence Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void outline_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showBoxes_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showText_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showColourText_actionPerformed()
{
caseChange = ChangeCaseCommand.TO_LOWER;
}
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + e.getActionCommand(), 600, 500);
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
String[] omitHidden = null;
System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
- // or we simply trust the user wants
- // wysiwig behaviour
+ // or we simply trust the user wants
+ // wysiwig behaviour
SequenceGroup sg = ap.av.getSelectionGroup();
ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
omitHidden = ap.av.getViewAsString(true);
Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
- for (int i = 0; i < nala.length; i++)
+ AlignmentAnnotation[] nala = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (nala != null)
{
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
+ for (int i = 0; i < nala.length; i++)
+ {
+ AlignmentAnnotation na = nala[i];
+ oal.addAnnotation(na);
+ }
}
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
oal, omitHidden, csel, sg));
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file");
- chooser.setToolTipText("Load a PDB file");
+ chooser.setDialogTitle("Select a PDB file for "
+ + sequence.getDisplayId(false));
+ chooser.setToolTipText("Load a PDB file and associate it with sequence '"
+ + sequence.getDisplayId(false) + "'");
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- PDBEntry entry = new PDBEntry();
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- try
- {
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
- jalview.io.AppletFormatAdapter.FILE);
-
- if (pdbfile.id == null)
- {
- String reply = JOptionPane
- .showInternalInputDialog(
- Desktop.desktop,
- "Couldn't find a PDB id in the file supplied."
- + "Please enter an Id to identify this structure.",
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
- if (reply == null)
- {
- return;
- }
-
- entry.setId(reply);
- }
- else
- {
- entry.setId(pdbfile.id);
- }
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
-
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, sequence, true);
}
}
public void discoverPDB_actionPerformed()
{
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+ : ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
public void run()
return;
}
- int rsize=0,gSize = sg.getSize();
- SequenceI[] rseqs,seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
-
+ 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)
+ if (start <= end)
{
seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
features[rsize] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
+ "Jalview");
rsize++;
}
}
rseqs = new SequenceI[rsize];
tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs,0,rseqs, 0, rsize);
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
System.arraycopy(features, 0, tfeatures, 0, rsize);
features = tfeatures;
seqs = rseqs;
public void colourByStructure(String pdbid)
{
- Annotation[] anots = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().colourSequenceFromStructure(
- sequence, pdbid);
+ Annotation[] anots = ap.av.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
AlignmentAnnotation an = new AlignmentAnnotation("Structure",
"Coloured by " + pdbid, anots);
- ap.av.alignment.addAnnotation(an);
+ ap.av.getAlignment().addAnnotation(an);
an.createSequenceMapping(sequence, 0, true);
// an.adjustForAlignment();
- ap.av.alignment.setAnnotationIndex(an, 0);
+ ap.av.getAlignment().setAnnotationIndex(an, 0);
ap.adjustAnnotationHeight();
if (sequence == null)
sequence = (Sequence) sg.getSequenceAt(0);
- EditNameDialog dialog = new EditNameDialog(sequence
- .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
- null, "Edit Sequence ", null, "Edit Sequence");
+ EditNameDialog dialog = new EditNameDialog(
+ sequence.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1), null, "Edit Sequence ", null,
+ "Edit Sequence", ap.alignFrame);
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.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
git://source.jalview.org / jalview.git / blobdiff