/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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
+public class PopupMenu extends JPopupMenu
{
JMenu groupMenu = new JMenu();
+
JMenuItem groupName = new JMenuItem();
+
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem hydrophobicityColour = new
- JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
AlignmentPanel ap;
+
JMenu sequenceMenu = new JMenu();
+
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+
+ SequenceI sequence;
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
+
JMenuItem outline = new JMenuItem();
+
JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+
JMenu colourMenu = new JMenu();
+
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
JMenu editMenu = new JMenu();
+
JMenuItem cut = new JMenuItem();
+
JMenuItem copy = new JMenuItem();
+
JMenuItem upperCase = new JMenuItem();
+
JMenuItem lowerCase = new JMenuItem();
+
JMenuItem toggle = new JMenuItem();
+
JMenu pdbMenu = new JMenu();
+
JMenuItem pdbFromFile = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
+
JMenuItem discoverPDB = new JMenuItem();
+
JMenu outputMenu = new JMenu();
+
JMenuItem sequenceFeature = new JMenuItem();
+
JMenuItem textColour = new JMenuItem();
+
JMenu jMenu1 = new JMenu();
+
JMenu structureMenu = new JMenu();
+
JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
+
+ // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
+
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+ JMenu groupLinksMenu;
/**
* Creates a new PopupMenu object.
- *
- * @param ap DOCUMENT ME!
- * @param seq DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
*/
public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
{
- ///////////////////////////////////////////////////////////
+ this(ap, seq, links, null);
+ }
+
+ /**
+ *
+ * @param ap
+ * @param seq
+ * @param links
+ * @param 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
// edit or annotate a particular residue. Therefore display the residue menu
//
// If from the IDPanel, we must display the sequence menu
- //////////////////////////////////////////////////////////
+ // ////////////////////////////////////////////////////////
this.ap = ap;
sequence = seq;
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++)
{
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
- i]);
+ JMenuItem item = new JMenuItem(
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
{
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
+ JMenuItem menuItem;
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- JMenuItem menuItem;
if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size()>0)
+ && seq.getDatasetSequence().getPDBId().size() > 0)
{
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
- elements();
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
+ .elements();
while (e.hasMoreElements())
{
{
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;
+ // 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);
+ }
- 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));
+ });
+ viewStructureMenu.add(menuItem);
- continue;
- }
- }
- }
+ /*
+ * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
+ * menuItem.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * colourByStructure(pdb.getId()); } });
+ * colStructureMenu.add(menuItem);
+ */
+ }
+ }
+ else
+ {
+ if (ap.av.getAlignment().isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
+ // structureMenu.remove(colStructureMenu);
+ }
- SequenceI [] seqs2 = new SequenceI[seqs.size()];
- seqs.toArray(seqs2);
+ 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);
+ }
+ }
- new AppJmol(pdb, seqs2, null, ap);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
- }
- });
- viewStructureMenu.add(menuItem);
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
- /* menuItem = new JMenuItem();
- menuItem.setText(pdb.getId());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
{
- public void actionPerformed(ActionEvent e)
+ if (seqAnno[i].getRNAStruc() != null)
{
- colourByStructure(pdb.getId());
+ 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);
}
- });
- colStructureMenu.add(menuItem);*/
+ }
}
- }
- else
- {
- structureMenu.remove(viewStructureMenu);
- // structureMenu.remove(colStructureMenu);
+
}
menuItem = new JMenuItem("Hide Sequences");
add(menuItem);
if (ap.av.getSelectionGroup() != null
- && ap.av.getSelectionGroup().getSize() > 1)
+ && ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem("Represent Group with " + seq.getName());
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)
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
menuItem = new JMenuItem("Reveal Sequences");
menuItem.addActionListener(new ActionListener()
});
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();
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
- if (sg != null)
- {
- groupName.setText(sg.getName());
+ if (sg != null && sg.getSize() > 0)
+ {
+ 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.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)
+ {
+ 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 (!isDefinedGroup)
{
+ createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
+ jMenu1.setText("Edit New Group");
+ } else {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText("Edit Group");
}
if (seq == null)
if (links != null && links.size() > 0)
{
+
JMenu linkMenu = new JMenu("Link");
- JMenuItem item;
+ Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
String link = links.elementAt(i).toString();
- final String label = link.substring(0, link.indexOf("|"));
- item = new JMenuItem(label);
- final String url;
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
{
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (seq != null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
+ // collect id string too
String id = seq.getName();
- if (id.indexOf("|") > -1)
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
{
- id = id.substring(id.lastIndexOf("|") + 1);
+ descr = null;
}
- url = link.substring(link.indexOf("|") + 1,
- link.indexOf("$SEQUENCE_ID$"))
- + id +
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ 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)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ 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)
+ {
+ if (!linkset.contains(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 link for this URL from description where regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
}
else
{
- url = link.substring(link.lastIndexOf("|") + 1);
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
+ {
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+ // Add a non-dynamic link
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ }
}
+ }
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+ {
- item.addActionListener(new java.awt.event.ActionListener()
+ // 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();
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+ Hashtable commonDbrefs = new Hashtable();
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
+
+ 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
+ SequenceI sqi = seqs[sq];
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
+ DBRefEntry[] dbr = sqi.getDBRef();
+ if (dbr != null && dbr.length > 0)
+ {
+ for (int d = 0; d < dbr.length; d++)
{
- public void actionPerformed(ActionEvent e)
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ Object[] sarray = (Object[]) commonDbrefs.get(src);
+ if (sarray == null)
{
- showLink(url);
+ sarray = new Object[2];
+ sarray[0] = new int[]
+ { 0 };
+ sarray[1] = new String[seqs.length];
+
+ commonDbrefs.put(src, sarray);
}
- });
- linkMenu.add(item);
+ 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 (sequence != null)
+ }
+ // 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
{
- sequenceMenu.add(linkMenu);
+ 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++)
+ {
+ if (allids[sq] != null)
+ {
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
+ }
+ }
}
else
{
- add(linkMenu);
+ // 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++)
+ {
+ 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
+ */
+ private void addshowLink(JMenu linkMenu, String label, final String url)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText("open URL: " + url);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ showLink(url);
+ }
+
+ }).start();
+ }
+ });
+
+ 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.
+ */
+ 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.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
* DOCUMENT ME!
- *
- * @throws Exception DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
*/
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
groupMenu.setText("Group");
groupMenu.setText("Selection");
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()
unGroupMenuItem_actionPerformed();
}
});
+ createGroupMenuItem.setText("Create Group");
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText("Border colour");
outline.addActionListener(new java.awt.event.ActionListener()
showColourText_actionPerformed();
}
});
+ displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
editMenu.setText("Edit");
cut.setText("Cut");
cut.addActionListener(new ActionListener()
jMenu1.setText("Group");
structureMenu.setText("Structure");
viewStructureMenu.setText("View Structure");
- // colStructureMenu.setText("Colour By Structure");
+ // colStructureMenu.setText("Colour By Structure");
editSequence.setText("Edit Sequence...");
editSequence.addActionListener(new ActionListener()
{
editSequence_actionPerformed(actionEvent);
}
});
- /* annotationMenuItem.setText("By Annotation");
- annotationMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- annotationMenuItem_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(outputMenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
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)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
- JMenuItem item = new JMenuItem(userColours.
- nextElement().toString());
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- //colourMenu.add(annotationMenuItem);
+ // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
+ // structureMenu.add(colStructureMenu);
noColourmenuItem.setText("None");
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
}
});
hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
helixColour.setText("Helix propensity");
helixColour.addActionListener(new java.awt.event.ActionListener()
{
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()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ }
+
+ 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().setShowNonconserved(displayNonconserved.isSelected());
+ refresh();
}
/**
- * DOCUMENT ME!
+ * call to refresh view after settings change
*/
void refresh()
{
+ ap.updateAnnotation();
ap.paintAlignment(true);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void zappoColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void taylorColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void hydrophobicityColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void helixColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void strandColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void turnColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void buriedColour_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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!
+ *
+ * @param e
+ * 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.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
- getGroup().getName());
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
- else // remove PIDColouring
+ else
+ // remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void userDefinedColour_actionPerformed(ActionEvent e)
{
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
sg.cs = udc;
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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!
+ *
+ * @param e
+ * 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!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
- else // remove ConservationColouring
+ else
+ // remove ConservationColouring
{
sg.cs.setConservation(null);
}
}
AnnotationColourGradient acg = new AnnotationColourGradient(
- sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+ sequence.getAnnotation()[0], null,
+ AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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");
+ sg.getDescription(), " Group Name ",
+ "Group Description ", "Edit Group Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
sg.setName(dialog.getName());
sg.setDescription(dialog.getDescription());
+ refresh();
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Get selection group - adding it to the alignment if necessary.
+ *
+ * @return sequence group to operate on
*/
SequenceGroup getGroup()
{
// 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!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(),
- " Sequence Name ",
- "Sequence Description ",
- "Edit Sequence Name/Description");
+ sequence.getDescription(), " Sequence Name ",
+ "Sequence Description ", "Edit Sequence Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
if (dialog.getName().indexOf(" ") > -1)
{
JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
- JOptionPane.WARNING_MESSAGE);
+ "Spaces have been converted to \"_\"",
+ "No spaces allowed in Sequence Name",
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * 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();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ refresh();
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
Color col = JColorChooser.showDialog(this, "Select Outline Colour",
- Color.BLUE);
+ Color.BLUE);
if (col != null)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void showBoxes_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void showText_actionPerformed()
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void showColourText_actionPerformed()
{
try
{
jalview.util.BrowserLauncher.openURL(url);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- +
- "\nAdd the full path to your browser in Preferences.",
- "Web browser not found",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Unixers: Couldn't find default web browser."
+ + "\nAdd the full path to your browser in Preferences.",
+ "Web browser not found", JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (sg == null || sg.getSize() < 1)
{
ap.av.hideSequence(new SequenceI[]
- {sequence});
+ { sequence });
return;
}
}
ap.av.hideSequence(hseqs);
+ // refresh(); TODO: ? needed ?
+ ap.av.sendSelection();
}
public void copy_actionPerformed()
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(
- sg.getStartRes(), sg.getEndRes() + 1);
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ sg.getEndRes() + 1);
String description;
int caseChange;
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);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600,
- 500);
+ "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
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ // 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));
- oal=null;
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ oal, omitHidden, csel, sg));
+ oal = null;
}
public void pdbFromFile_actionPerformed()
{
- jalview.io.JalviewFileChooser chooser
- = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ 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 enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
PDBEntry entry = new PDBEntry();
entry.setId(id.toUpperCase());
- sequence.getDatasetSequence()
- .addPDBId(entry);
+ sequence.getDatasetSequence().addPDBId(entry);
}
}
public void discoverPDB_actionPerformed()
{
- SequenceI[] sequences =
- ap.av.selectionGroup == null ?
- new Sequence[]{sequence}
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
- new jalview.ws.DBRefFetcher(sequences,
- ap.alignFrame).fetchDBRefs(false);
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ Thread discpdb = new Thread(new Runnable()
+ {
+ public void run()
+ {
+
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+ .fetchDBRefs(false);
+ }
+
+ });
+ discpdb.start();
}
public void sequenceFeature_actionPerformed()
return;
}
- int gSize = sg.getSize();
- SequenceI[] seqs = new SequenceI[gSize];
- SequenceFeature[] 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++)
{
- seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
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 (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
+ features[rsize] = new SequenceFeature(null, null, null, start, end,
+ "Jalview");
+ rsize++;
+ }
}
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
- {
- ap.alignFrame.showSeqFeatures.setSelected(true);
- ap.av.setShowSequenceFeatures(true);
+ 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.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
}
}
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);
+ 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);
+ // an.adjustForAlignment();
+ ap.av.getAlignment().setAnnotationIndex(an, 0);
ap.adjustAnnotationHeight();
sequence.addAlignmentAnnotation(an);
- }
+ }
public void editSequence_actionPerformed(ActionEvent actionEvent)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
+ SequenceGroup sg = ap.av.getSelectionGroup();
- if(sg!=null)
- {
- if (sequence == null)
- sequence = (Sequence) sg.getSequenceAt(0);
+ if (sg != null)
+ {
+ 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
- );
+ 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.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
+ }
}
-
}
git://source.jalview.org / jalview.git / blobdiff