/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.gui;\r
\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import javax.swing.*;\r
\r
-import MCview.*;\r
import jalview.analysis.*;\r
import jalview.commands.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
import jalview.schemes.*;\r
+import jalview.util.GroupUrlLink;\r
+import jalview.util.GroupUrlLink.UrlStringTooLongException;\r
+import jalview.util.MessageManager;\r
+import jalview.util.UrlLink;\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
+ * \r
* @author $author$\r
- * @version $Revision$\r
+ * @version $Revision: 1.118 $\r
*/\r
-public class PopupMenu\r
- extends JPopupMenu\r
+public class PopupMenu extends JPopupMenu\r
{\r
JMenu groupMenu = new JMenu();\r
+\r
JMenuItem groupName = new JMenuItem();\r
+\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new\r
- JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
+\r
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
+\r
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
+\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();\r
+\r
+ // protected JRadioButtonMenuItem covariationColour = new\r
+ // JRadioButtonMenuItem();\r
+\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
+\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+\r
AlignmentPanel ap;\r
+\r
JMenu sequenceMenu = new JMenu();\r
+\r
JMenuItem sequenceName = new JMenuItem();\r
- Sequence sequence;\r
+\r
+ JMenuItem sequenceDetails = new JMenuItem();\r
+\r
+ JMenuItem sequenceSelDetails = new JMenuItem();\r
+\r
+ SequenceI sequence;\r
+ JMenuItem createGroupMenuItem = new JMenuItem();\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
+\r
JMenuItem outline = new JMenuItem();\r
+\r
JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
+\r
JMenu colourMenu = new JMenu();\r
+\r
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+\r
JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+\r
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
+\r
JMenu editMenu = new JMenu();\r
+\r
JMenuItem cut = new JMenuItem();\r
+\r
JMenuItem copy = new JMenuItem();\r
+\r
JMenuItem upperCase = new JMenuItem();\r
+\r
JMenuItem lowerCase = new JMenuItem();\r
+\r
JMenuItem toggle = new JMenuItem();\r
+\r
JMenu pdbMenu = new JMenu();\r
+\r
JMenuItem pdbFromFile = new JMenuItem();\r
+\r
JMenuItem enterPDB = new JMenuItem();\r
+\r
JMenuItem discoverPDB = new JMenuItem();\r
+\r
JMenu outputMenu = new JMenu();\r
+\r
JMenuItem sequenceFeature = new JMenuItem();\r
+\r
JMenuItem textColour = new JMenuItem();\r
+\r
JMenu jMenu1 = new JMenu();\r
\r
+ JMenu structureMenu = new JMenu();\r
+\r
+ JMenu viewStructureMenu = new JMenu();\r
+\r
+ // JMenu colStructureMenu = new JMenu();\r
+ JMenuItem editSequence = new JMenuItem();\r
+\r
+ // JMenuItem annotationMenuItem = new JMenuItem();\r
+\r
+ JMenu groupLinksMenu;\r
+\r
/**\r
* Creates a new PopupMenu object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
+ * \r
+ * @param ap\r
+ * DOCUMENT ME!\r
+ * @param seq\r
+ * DOCUMENT ME!\r
*/\r
public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
{\r
- ///////////////////////////////////////////////////////////\r
+ this(ap, seq, links, null);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param ap\r
+ * @param seq\r
+ * @param links\r
+ * @param groupLinks\r
+ */\r
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,\r
+ Vector links, Vector groupLinks)\r
+ {\r
+ // /////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
// edit or annotate a particular residue. Therefore display the residue menu\r
//\r
// If from the IDPanel, we must display the sequence menu\r
- //////////////////////////////////////////////////////////\r
+ // ////////////////////////////////////////////////////////\r
this.ap = ap;\r
sequence = seq;\r
\r
colours.add(userDefinedColour);\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
+ colours.add(purinePyrimidineColour);\r
+ // colours.add(covariationColour);\r
\r
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
- i]);\r
+ JMenuItem item = new JMenuItem(\r
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);\r
\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
try\r
{\r
jbInit();\r
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
e.printStackTrace();\r
}\r
\r
+ JMenuItem menuItem;\r
if (seq != null)\r
{\r
sequenceMenu.setText(sequence.getName());\r
\r
- JMenuItem menuItem;\r
- if (seq.getDatasetSequence().getPDBId() != null)\r
+ if (seq.getDatasetSequence().getPDBId() != null\r
+ && seq.getDatasetSequence().getPDBId().size() > 0)\r
{\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
- elements();\r
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId()\r
+ .elements();\r
\r
while (e.hasMoreElements())\r
{\r
final PDBEntry pdb = (PDBEntry) e.nextElement();\r
\r
menuItem = new JMenuItem();\r
- menuItem.setText("View PDB entry: " + pdb.getId());\r
+ menuItem.setText(pdb.getId());\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
+ // TODO re JAL-860: optionally open dialog or provide a menu entry\r
+ // allowing user to open just one structure per sequence\r
+ new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]\r
+ { pdb })[0], null, ap);\r
+ // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
+ }\r
\r
- Vector seqs = new Vector();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
+\r
+ /*\r
+ * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());\r
+ * menuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ * public void actionPerformed(ActionEvent e) {\r
+ * colourByStructure(pdb.getId()); } });\r
+ * colStructureMenu.add(menuItem);\r
+ */\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (ap.av.getAlignment().isNucleotide() == false)\r
+ {\r
+ structureMenu.remove(viewStructureMenu);\r
+ }\r
+ // structureMenu.remove(colStructureMenu);\r
+ }\r
+\r
+ if (ap.av.getAlignment().isNucleotide() == true)\r
+ {\r
+ AlignmentAnnotation[] aa = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].getRNAStruc() != null)\r
+ {\r
+ final String rnastruc = aa[i].getRNAStruc();\r
+ final String structureLine = aa[i].label;\r
+ menuItem = new JMenuItem();\r
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
- if(pdbs==null)\r
- continue;\r
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),\r
+ rnastruc, seq.getName(), ap);\r
+ }\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
+ }\r
+ }\r
\r
- for(int p=0; p<pdbs.size(); p++)\r
- {\r
- PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
- if(p1.getId().equals(pdb.getId()))\r
- {\r
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
- seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
+ // SequenceFeatures[] test = seq.getSequenceFeatures();\r
\r
- continue;\r
- }\r
+ if (seq.getAnnotation() != null)\r
+ {\r
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();\r
+ for (int i = 0; i < seqAnno.length; i++)\r
+ {\r
+ if (seqAnno[i].getRNAStruc() != null)\r
+ {\r
+ final String rnastruc = seqAnno[i].getRNAStruc();\r
\r
+ // TODO: make rnastrucF a bit more nice\r
+ menuItem = new JMenuItem();\r
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO: VARNA does'nt print gaps in the sequence\r
+ new AppVarna(seq.getName() + " structure", seq, seq\r
+ .getSequenceAsString(), rnastruc, seq.getName(),\r
+ ap);\r
}\r
- }\r
-\r
- SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
- seqs.toArray(seqs2);\r
-\r
- new AppJMol(pdb, seqs2, ap);\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
}\r
- });\r
- sequenceMenu.add(menuItem);\r
+ }\r
}\r
+\r
}\r
\r
- menuItem = new JMenuItem("Hide Sequences");\r
+ menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
add(menuItem);\r
\r
if (ap.av.getSelectionGroup() != null\r
- && ap.av.getSelectionGroup().getSize() > 1)\r
+ && ap.av.getSelectionGroup().getSize() > 1)\r
{\r
- menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
+ menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sequenceMenu.add(menuItem);\r
}\r
\r
- if (ap.av.hasHiddenRows)\r
+ if (ap.av.hasHiddenRows())\r
{\r
- final int index = ap.av.alignment.findIndex(seq);\r
+ final int index = ap.av.getAlignment().findIndex(seq);\r
\r
- if (ap.av.adjustForHiddenSeqs(index) -\r
- ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
+ if (ap.av.adjustForHiddenSeqs(index)\r
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
{\r
- menuItem = new JMenuItem("Reveal Sequences");\r
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
menuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
});\r
add(menuItem);\r
}\r
-\r
- menuItem = new JMenuItem("Reveal All");\r
+ }\r
+ }\r
+ // for the case when no sequences are even visible\r
+ if (ap.av.hasHiddenRows())\r
+ {\r
+ {\r
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
menuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;\r
\r
- if (sg != null)\r
- {\r
- groupName.setText(sg.getName());\r
+ if (sg != null && sg.getSize() > 0)\r
+ { \r
+ groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
+ groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
\r
if (sg.cs instanceof ZappoColourScheme)\r
{\r
{\r
clustalColour.setSelected(true);\r
}\r
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
+ {\r
+ purinePyrimidineColour.setSelected(true);\r
+ }\r
+ /*\r
+ * else if (sg.cs instanceof CovariationColourScheme) {\r
+ * covariationColour.setSelected(true); }\r
+ */\r
else\r
{\r
noColourmenuItem.setSelected(true);\r
{\r
conservationMenuItem.setSelected(true);\r
}\r
-\r
+ displayNonconserved.setSelected(sg.getShowNonconserved());\r
showText.setSelected(sg.getDisplayText());\r
showColourText.setSelected(sg.getColourText());\r
showBoxes.setSelected(sg.getDisplayBoxes());\r
+ // add any groupURLs to the groupURL submenu and make it visible\r
+ if (groupLinks != null && groupLinks.size() > 0)\r
+ {\r
+ buildGroupURLMenu(sg, groupLinks);\r
+ }\r
+ // Add a 'show all structures' for the current selection\r
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
+ SequenceI sqass = null;\r
+ for (SequenceI sq : ap.av.getSequenceSelection())\r
+ {\r
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
+ .getPDBId();\r
+ if (pes != null)\r
+ {\r
+ for (PDBEntry pe : pes)\r
+ {\r
+ pdbe.put(pe.getId(), pe);\r
+ if (sqass == null)\r
+ {\r
+ sqass = sq;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (pdbe.size() > 0)\r
+ {\r
+ final PDBEntry[] pe = pdbe.values().toArray(\r
+ new PDBEntry[pdbe.size()]);\r
+ final JMenuItem gpdbview;\r
+ if (pdbe.size() == 1)\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
+ }\r
+ else\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
+ }\r
+ gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
+ gpdbview.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new AppJmol(ap, pe, ap.av.collateForPDB(pe));\r
+ }\r
+ });\r
+ }\r
}\r
else\r
{\r
editMenu.setVisible(false);\r
}\r
\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
+ if (!isDefinedGroup)\r
{\r
+ createGroupMenuItem.setVisible(true);\r
unGroupMenuItem.setVisible(false);\r
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
+ } else {\r
+ createGroupMenuItem.setVisible(false);\r
+ unGroupMenuItem.setVisible(true);\r
+ jMenu1.setText(MessageManager.getString("action.edit_group"));\r
}\r
\r
if (seq == null)\r
{\r
sequenceMenu.setVisible(false);\r
- pdbMenu.setVisible(false);\r
+ structureMenu.setVisible(false);\r
}\r
\r
if (links != null && links.size() > 0)\r
{\r
- JMenu linkMenu = new JMenu("Link");\r
- JMenuItem item;\r
+\r
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
+ Vector linkset = new Vector();\r
for (int i = 0; i < links.size(); i++)\r
{\r
String link = links.elementAt(i).toString();\r
- final String label = link.substring(0, link.indexOf("|"));\r
- item = new JMenuItem(label);\r
- final String url;\r
-\r
- if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+ UrlLink urlLink = null;\r
+ try\r
+ {\r
+ urlLink = new UrlLink(link);\r
+ } catch (Exception foo)\r
{\r
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link\r
+ + "'", foo);\r
+ continue;\r
+ }\r
+ ;\r
+ if (!urlLink.isValid())\r
+ {\r
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
+ continue;\r
+ }\r
+ final String label = urlLink.getLabel();\r
+ if (seq != null && urlLink.isDynamic())\r
+ {\r
+\r
+ // collect matching db-refs\r
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(\r
+ seq.getDBRef(), new String[]\r
+ { urlLink.getTarget() });\r
+ // collect id string too\r
String id = seq.getName();\r
- if (id.indexOf("|") > -1)\r
+ String descr = seq.getDescription();\r
+ if (descr != null && descr.length() < 1)\r
{\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
+ descr = null;\r
}\r
\r
- url = link.substring(link.indexOf("|") + 1,\r
- link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ if (dbr != null)\r
+ {\r
+ for (int r = 0; r < dbr.length; r++)\r
+ {\r
+ if (id != null && dbr[r].getAccessionId().equals(id))\r
+ {\r
+ // suppress duplicate link creation for the bare sequence ID\r
+ // string with this link\r
+ id = null;\r
+ }\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
+ true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label + "|" + urls[u],\r
+ urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (id != null)\r
+ {\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(id, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // Create urls from description but only for URL links which are regex\r
+ // links\r
+ if (descr != null && urlLink.getRegexReplace() != null)\r
+ {\r
+ // create link for this URL from description where regex matches\r
+ String[] urls = urlLink.makeUrls(descr, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
else\r
{\r
- url = link.substring(link.lastIndexOf("|") + 1);\r
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))\r
+ {\r
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());\r
+ // Add a non-dynamic link\r
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());\r
+ }\r
}\r
+ }\r
+ if (sequence != null)\r
+ {\r
+ sequenceMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
+ }\r
+ }\r
\r
- item.addActionListener(new java.awt.event.ActionListener()\r
+ private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)\r
+ {\r
+\r
+ // TODO: usability: thread off the generation of group url content so root\r
+ // menu appears asap\r
+ // sequence only URLs\r
+ // ID/regex match URLs\r
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ JMenu[] linkMenus = new JMenu[]\r
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
+ // created.\r
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();\r
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);\r
+ Hashtable commonDbrefs = new Hashtable();\r
+ for (int sq = 0; sq < seqs.length; sq++)\r
+ {\r
+\r
+ int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]\r
+ .findPosition(sg.getEndRes());\r
+ // just collect ids from dataset sequence\r
+ // TODO: check if IDs collected from selecton group intersects with the\r
+ // current selection, too\r
+ SequenceI sqi = seqs[sq];\r
+ while (sqi.getDatasetSequence() != null)\r
+ {\r
+ sqi = sqi.getDatasetSequence();\r
+ }\r
+ DBRefEntry[] dbr = sqi.getDBRef();\r
+ if (dbr != null && dbr.length > 0)\r
+ {\r
+ for (int d = 0; d < dbr.length; d++)\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();\r
+ Object[] sarray = (Object[]) commonDbrefs.get(src);\r
+ if (sarray == null)\r
{\r
- showLink(url);\r
+ sarray = new Object[2];\r
+ sarray[0] = new int[]\r
+ { 0 };\r
+ sarray[1] = new String[seqs.length];\r
+\r
+ commonDbrefs.put(src, sarray);\r
}\r
- });\r
\r
- linkMenu.add(item);\r
+ if (((String[]) sarray[1])[sq] == null)\r
+ {\r
+ if (!dbr[d].hasMap()\r
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))\r
+ {\r
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();\r
+ ((int[]) sarray[0])[0]++;\r
+ }\r
+ }\r
+ }\r
}\r
- if (sequence != null)\r
+ }\r
+ // now create group links for all distinct ID/sequence sets.\r
+ boolean addMenu = false; // indicates if there are any group links to give\r
+ // to user\r
+ for (int i = 0; i < groupLinks.size(); i++)\r
+ {\r
+ String link = groupLinks.elementAt(i).toString();\r
+ GroupUrlLink urlLink = null;\r
+ try\r
{\r
- sequenceMenu.add(linkMenu);\r
+ urlLink = new GroupUrlLink(link);\r
+ } catch (Exception foo)\r
+ {\r
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link\r
+ + "'", foo);\r
+ continue;\r
+ }\r
+ ;\r
+ if (!urlLink.isValid())\r
+ {\r
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
+ continue;\r
+ }\r
+ final String label = urlLink.getLabel();\r
+ boolean usingNames = false;\r
+ // Now see which parts of the group apply for this URL\r
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());\r
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());\r
+ String[] seqstr, ids; // input to makeUrl\r
+ if (idset != null)\r
+ {\r
+ int numinput = ((int[]) idset[0])[0];\r
+ String[] allids = ((String[]) idset[1]);\r
+ seqstr = new String[numinput];\r
+ ids = new String[numinput];\r
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)\r
+ {\r
+ if (allids[sq] != null)\r
+ {\r
+ ids[idcount] = allids[sq];\r
+ seqstr[idcount++] = idandseqs[1][sq];\r
+ }\r
+ }\r
}\r
else\r
{\r
- add(linkMenu);\r
+ // just use the id/seq set\r
+ seqstr = idandseqs[1];\r
+ ids = idandseqs[0];\r
+ usingNames = true;\r
+ }\r
+ // and try and make the groupURL!\r
+\r
+ Object[] urlset = null;\r
+ try\r
+ {\r
+ urlset = urlLink.makeUrlStubs(ids, seqstr,\r
+ "FromJalview" + System.currentTimeMillis(), false);\r
+ } catch (UrlStringTooLongException e)\r
+ {\r
+ }\r
+ if (urlset != null)\r
+ {\r
+ int type = urlLink.getGroupURLType() & 3;\r
+ // System.out.println(urlLink.getGroupURLType()\r
+ // +" "+((String[])urlset[3])[0]);\r
+ // first two bits ofurlLink type bitfield are sequenceids and sequences\r
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised\r
+ addshowLink(linkMenus[type], label\r
+ + (((type & 1) == 1) ? ("("\r
+ + (usingNames ? "Names" : ltarget) + ")") : ""),\r
+ urlLink, urlset);\r
+ addMenu = true;\r
}\r
}\r
+ if (addMenu)\r
+ {\r
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ for (int m = 0; m < linkMenus.length; m++)\r
+ {\r
+ if (linkMenus[m] != null\r
+ && linkMenus[m].getMenuComponentCount() > 0)\r
+ {\r
+ groupLinksMenu.add(linkMenus[m]);\r
+ }\r
+ }\r
+\r
+ groupMenu.add(groupLinksMenu);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * add a show URL menu item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param label\r
+ * - menu label string\r
+ * @param url\r
+ * - url to open\r
+ */\r
+ private void addshowLink(JMenu linkMenu, String label, final String url)\r
+ {\r
+ JMenuItem item = new JMenuItem(label);\r
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ public void run()\r
+ {\r
+ showLink(url);\r
+ }\r
+\r
+ }).start();\r
+ }\r
+ });\r
+\r
+ linkMenu.add(item);\r
+ }\r
+\r
+ /**\r
+ * add a late bound groupURL item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param label\r
+ * - menu label string\r
+ * @param urlgenerator\r
+ * GroupURLLink used to generate URL\r
+ * @param urlstub\r
+ * Object array returned from the makeUrlStubs function.\r
+ */\r
+ private void addshowLink(JMenu linkMenu, String label,\r
+ final GroupUrlLink urlgenerator, final Object[] urlstub)\r
+ {\r
+ JMenuItem item = new JMenuItem(label);\r
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
+ // TODO: put in info about what is being sent.\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ showLink(urlgenerator.constructFrom(urlstub));\r
+ } catch (UrlStringTooLongException e)\r
+ {\r
+ }\r
+ }\r
+\r
+ }).start();\r
+ }\r
+ });\r
+\r
+ linkMenu.add(item);\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
+ * \r
+ * @throws Exception\r
+ * DOCUMENT ME!\r
*/\r
- private void jbInit()\r
- throws Exception\r
+ private void jbInit() throws Exception\r
{\r
- groupMenu.setText("Group");\r
- groupMenu.setText("Selection");\r
- groupName.setText("Name");\r
+ groupMenu.setText(MessageManager.getString("label.group"));\r
+ groupMenu.setText(MessageManager.getString("label.selection"));\r
+ groupName.setText(MessageManager.getString("label.name"));\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
groupName_actionPerformed();\r
}\r
});\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit Name/Description");\r
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
+ sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sequenceName_actionPerformed();\r
}\r
});\r
+ sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceDetails_actionPerformed();\r
+ }\r
+ });\r
+ sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceSelDetails\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceSelectionDetails_actionPerformed();\r
+ }\r
+ });\r
PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText("Remove Group");\r
+ unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
unGroupMenuItem_actionPerformed();\r
}\r
});\r
+ createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createGroupMenuItem_actionPerformed();\r
+ }\r
+ });\r
\r
- outline.setText("Border colour");\r
+ outline.setText(MessageManager.getString("action.border_colour"));\r
outline.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
outline_actionPerformed();\r
}\r
});\r
- nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
nucleotideMenuItem_actionPerformed();\r
}\r
});\r
- colourMenu.setText("Group Colour");\r
- showBoxes.setText("Boxes");\r
+ colourMenu.setText(MessageManager.getString("label.group_colour"));\r
+ showBoxes.setText(MessageManager.getString("action.boxes"));\r
showBoxes.setState(true);\r
showBoxes.addActionListener(new ActionListener()\r
{\r
showBoxes_actionPerformed();\r
}\r
});\r
- showText.setText("Text");\r
+ showText.setText(MessageManager.getString("action.text"));\r
showText.setState(true);\r
showText.addActionListener(new ActionListener()\r
{\r
showText_actionPerformed();\r
}\r
});\r
- showColourText.setText("Colour Text");\r
+ showColourText.setText(MessageManager.getString("label.colour_text"));\r
showColourText.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
showColourText_actionPerformed();\r
}\r
});\r
- editMenu.setText("Edit");\r
- cut.setText("Cut");\r
+ displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
+ displayNonconserved.setState(true);\r
+ displayNonconserved.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showNonconserved_actionPerformed();\r
+ }\r
+ });\r
+ editMenu.setText(MessageManager.getString("action.edit"));\r
+ cut.setText(MessageManager.getString("action.cut"));\r
cut.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
cut_actionPerformed();\r
}\r
});\r
- upperCase.setText("To Upper Case");\r
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
upperCase.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
changeCase(e);\r
}\r
});\r
- copy.setText("Copy");\r
+ copy.setText(MessageManager.getString("action.copy"));\r
copy.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
copy_actionPerformed();\r
}\r
});\r
- lowerCase.setText("To Lower Case");\r
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
lowerCase.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
changeCase(e);\r
}\r
});\r
- toggle.setText("Toggle Case");\r
+ toggle.setText(MessageManager.getString("label.toggle_case"));\r
toggle.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
changeCase(e);\r
}\r
});\r
- pdbMenu.setText("Associate Structure with Sequence");\r
- pdbFromFile.setText("From File");\r
+ pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
pdbFromFile.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
pdbFromFile_actionPerformed();\r
}\r
});\r
- enterPDB.setText("Enter PDB Id");\r
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
enterPDB.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
enterPDB_actionPerformed();\r
}\r
});\r
- discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
discoverPDB.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
discoverPDB_actionPerformed();\r
}\r
});\r
- outputMenu.setText("Output to Textbox...");\r
- sequenceFeature.setText("Create Sequence Feature");\r
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
+ sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
sequenceFeature.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sequenceFeature_actionPerformed();\r
}\r
});\r
- textColour.setText("Text Colour");\r
+ textColour.setText(MessageManager.getString("label.text_colour"));\r
textColour.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
textColour_actionPerformed();\r
}\r
});\r
- jMenu1.setText("Group");\r
- add(groupMenu);\r
+ jMenu1.setText(MessageManager.getString("label.group"));\r
+ structureMenu.setText(MessageManager.getString("label.structure"));\r
+ viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
+ // colStructureMenu.setText("Colour By Structure");\r
+ editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
+ editSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ editSequence_actionPerformed(actionEvent);\r
+ }\r
+ });\r
\r
+ /*\r
+ * annotationMenuItem.setText("By Annotation");\r
+ * annotationMenuItem.addActionListener(new ActionListener() { public void\r
+ * actionPerformed(ActionEvent actionEvent) {\r
+ * annotationMenuItem_actionPerformed(actionEvent); } });\r
+ */\r
+ groupMenu.add(sequenceSelDetails);\r
+ add(groupMenu);\r
add(sequenceMenu);\r
+ this.add(structureMenu);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputMenu);\r
groupMenu.add(sequenceFeature);\r
+ groupMenu.add(createGroupMenuItem);\r
+ groupMenu.add(unGroupMenuItem);\r
groupMenu.add(jMenu1);\r
sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(pdbMenu);\r
+ sequenceMenu.add(sequenceDetails);\r
colourMenu.add(textColour);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(turnColour);\r
colourMenu.add(buriedColour);\r
colourMenu.add(nucleotideMenuItem);\r
+ if (ap.getAlignment().isNucleotide())\r
+ {\r
+ colourMenu.add(purinePyrimidineColour);\r
+ }\r
+ // colourMenu.add(covariationColour);\r
colourMenu.add(userDefinedColour);\r
\r
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
{\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours\r
+ .getUserColourSchemes().keys();\r
\r
while (userColours.hasMoreElements())\r
{\r
- JMenuItem item = new JMenuItem(userColours.\r
- nextElement().toString());\r
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());\r
item.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent evt)\r
colourMenu.addSeparator();\r
colourMenu.add(abovePIDColour);\r
colourMenu.add(conservationMenuItem);\r
+ // colourMenu.add(annotationMenuItem);\r
editMenu.add(copy);\r
editMenu.add(cut);\r
+ editMenu.add(editSequence);\r
editMenu.add(upperCase);\r
editMenu.add(lowerCase);\r
editMenu.add(toggle);\r
pdbMenu.add(enterPDB);\r
pdbMenu.add(discoverPDB);\r
jMenu1.add(groupName);\r
- jMenu1.add(unGroupMenuItem);\r
jMenu1.add(colourMenu);\r
jMenu1.add(showBoxes);\r
jMenu1.add(showText);\r
jMenu1.add(showColourText);\r
jMenu1.add(outline);\r
- noColourmenuItem.setText("None");\r
+ jMenu1.add(displayNonconserved);\r
+ structureMenu.add(pdbMenu);\r
+ structureMenu.add(viewStructureMenu);\r
+ // structureMenu.add(colStructureMenu);\r
+ noColourmenuItem.setText(MessageManager.getString("label.none"));\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- clustalColour.setText("Clustalx colours");\r
+ clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
clustalColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
clustalColour_actionPerformed();\r
}\r
});\r
- zappoColour.setText("Zappo");\r
+ zappoColour.setText(MessageManager.getString("label.zappo"));\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
zappoColour_actionPerformed();\r
}\r
});\r
- taylorColour.setText("Taylor");\r
+ taylorColour.setText(MessageManager.getString("label.taylor"));\r
taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
taylorColour_actionPerformed();\r
}\r
});\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
+ hydrophobicityColour\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hydrophobicityColour_actionPerformed();\r
+ }\r
+ });\r
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
helixColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
helixColour_actionPerformed();\r
}\r
});\r
- strandColour.setText("Strand propensity");\r
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
strandColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
strandColour_actionPerformed();\r
}\r
});\r
- turnColour.setText("Turn propensity");\r
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
turnColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
turnColour_actionPerformed();\r
}\r
});\r
- buriedColour.setText("Buried Index");\r
+ buriedColour.setText(MessageManager.getString("label.buried_index"));\r
buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
buriedColour_actionPerformed();\r
}\r
});\r
- abovePIDColour.setText("Above % Identity");\r
+ abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDColour_actionPerformed();\r
}\r
});\r
- userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
userDefinedColour_actionPerformed(e);\r
}\r
});\r
- PIDColour.setText("Percentage Identity");\r
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
PIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed();\r
}\r
});\r
- BLOSUM62Colour.setText("BLOSUM62");\r
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed();\r
}\r
});\r
- conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
+ purinePyrimidineColour\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ purinePyrimidineColour_actionPerformed();\r
+ }\r
+ });\r
+ /*\r
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {\r
+ * public void actionPerformed(ActionEvent e) {\r
+ * covariationColour_actionPerformed(); } });\r
+ */\r
+\r
+ conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
+ conservationMenuItem\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ });\r
+ }\r
+\r
+ protected void sequenceSelectionDetails_actionPerformed()\r
+ {\r
+ createSequenceDetailsReport(ap.av.getSequenceSelection());\r
+ }\r
+\r
+ protected void sequenceDetails_actionPerformed()\r
+ {\r
+ createSequenceDetailsReport(new SequenceI[]\r
+ { sequence });\r
+ }\r
+\r
+ public void createSequenceDetailsReport(SequenceI[] sequences)\r
+ {\r
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();\r
+ StringBuffer contents = new StringBuffer();\r
+ for (SequenceI seq : sequences)\r
+ { \r
+ contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
+ + "</h2></p><p>");\r
+ new SequenceAnnotationReport(null)\r
+ .createSequenceAnnotationReport(\r
+ contents,\r
+ seq,\r
+ true,\r
+ true,\r
+ false,\r
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax\r
+ : null);\r
+ contents.append("</p>");\r
+ }\r
+ cap.setText("<html>" + contents.toString() + "</html>");\r
+\r
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
+ ,500, 400);\r
+\r
+ }\r
+\r
+ protected void showNonconserved_actionPerformed()\r
+ {\r
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());\r
+ refresh();\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * call to refresh view after settings change\r
*/\r
void refresh()\r
{\r
+ ap.updateAnnotation();\r
ap.paintAlignment(true);\r
\r
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
- ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
refresh();\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void zappoColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void taylorColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void hydrophobicityColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void helixColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void strandColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void turnColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void buriedColour_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
public void nucleotideMenuItem_actionPerformed()\r
{\r
refresh();\r
}\r
\r
+ protected void purinePyrimidineColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new PurinePyrimidineColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /*\r
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new\r
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }\r
+ */\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void abovePIDColour_actionPerformed()\r
{\r
if (abovePIDColour.isSelected())\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
+ .getName());\r
\r
sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
SliderPanel.showPIDSlider();\r
}\r
- else // remove PIDColouring\r
+ else\r
+ // remove PIDColouring\r
{\r
sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- if (e.getActionCommand().equals("User Defined..."))\r
+ if (e.getSource().equals(userDefinedColour))\r
{\r
new UserDefinedColours(ap, sg);\r
}\r
else\r
{\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
+ .getUserColourSchemes().get(e.getActionCommand());\r
\r
sg.cs = udc;\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void PIDColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void BLOSUM62Colour_actionPerformed()\r
{\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void noColourmenuItem_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void conservationMenuItem_actionPerformed()\r
{\r
\r
if (conservationMenuItem.isSelected())\r
{\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
+ Conservation c = new Conservation(MessageManager.getString("label.group"),\r
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
+ c.verdict(false, ap.av.getConsPercGaps());\r
\r
sg.cs.setConservation(c);\r
\r
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
SliderPanel.showConservationSlider();\r
}\r
- else // remove ConservationColouring\r
+ else\r
+ // remove ConservationColouring\r
{\r
sg.cs.setConservation(null);\r
}\r
refresh();\r
}\r
\r
+ public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ AnnotationColourGradient acg = new AnnotationColourGradient(\r
+ sequence.getAnnotation()[0], null,\r
+ AnnotationColourGradient.NO_THRESHOLD);\r
+\r
+ acg.setPredefinedColours(true);\r
+ sg.cs = acg;\r
+\r
+ refresh();\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void groupName_actionPerformed()\r
{\r
\r
SequenceGroup sg = getGroup();\r
EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
- sg.getDescription(),\r
- " Group Name ",\r
- "Group Description ",\r
- "Edit Group Name/Description");\r
+ sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
+ MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
+ ap.alignFrame);\r
\r
if (!dialog.accept)\r
{\r
\r
sg.setName(dialog.getName());\r
sg.setDescription(dialog.getDescription());\r
+ refresh();\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Get selection group - adding it to the alignment if necessary.\r
+ * \r
+ * @return sequence group to operate on\r
*/\r
SequenceGroup getGroup()\r
{\r
// this method won't add a new group if it already exists\r
if (sg != null)\r
{\r
- ap.av.alignment.addGroup(sg);\r
+ ap.av.getAlignment().addGroup(sg);\r
}\r
\r
return sg;\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
void sequenceName_actionPerformed()\r
{\r
EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(),\r
- " Sequence Name ",\r
- "Sequence Description ",\r
- "Edit Sequence Name/Description");\r
+ sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
+ MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
+ ap.alignFrame);\r
\r
if (!dialog.accept)\r
{\r
if (dialog.getName().indexOf(" ") > -1)\r
{\r
JOptionPane.showMessageDialog(ap,\r
- "Spaces have been converted to \"_\"",\r
- "No spaces allowed in Sequence Name",\r
- JOptionPane.WARNING_MESSAGE);\r
+ MessageManager.getString("label.spaces_converted_to_backslashes"),\r
+ MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
+ JOptionPane.WARNING_MESSAGE);\r
}\r
\r
sequence.setName(dialog.getName().replace(' ', '_'));\r
\r
sequence.setDescription(dialog.getDescription());\r
\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
void unGroupMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
+ ap.av.getAlignment().deleteGroup(sg);\r
ap.av.setSelectionGroup(null);\r
refresh();\r
}\r
+ void createGroupMenuItem_actionPerformed()\r
+ {\r
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this\r
+ refresh();\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void outline_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
- Color.BLUE);\r
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
+ Color.BLUE);\r
\r
if (col != null)\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
public void showBoxes_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
public void showText_actionPerformed()\r
{\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
public void showColourText_actionPerformed()\r
{\r
try\r
{\r
jalview.util.BrowserLauncher.openURL(url);\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Unixers: Couldn't find default web browser."\r
- +\r
- "\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found",\r
- JOptionPane.WARNING_MESSAGE);\r
+ JOptionPane\r
+ .showInternalMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.web_browser_not_found_unix"),\r
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
\r
ex.printStackTrace();\r
}\r
if (sg == null || sg.getSize() < 1)\r
{\r
ap.av.hideSequence(new SequenceI[]\r
- {sequence});\r
+ { sequence });\r
return;\r
}\r
\r
}\r
\r
ap.av.hideSequence(hseqs);\r
+ // refresh(); TODO: ? needed ?\r
+ ap.av.sendSelection();\r
}\r
\r
public void copy_actionPerformed()\r
\r
if (sg != null)\r
{\r
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(\r
- sg.getStartRes(), sg.getEndRes() + 1);\r
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
String description;\r
int caseChange;\r
\r
if (source == toggle)\r
{\r
- description = "Toggle Case";\r
+ description = MessageManager.getString("label.toggle_case");\r
caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
}\r
else if (source == upperCase)\r
{\r
- description = "To Upper Case";\r
+ description = MessageManager.getString("label.to_upper_case");\r
caseChange = ChangeCaseCommand.TO_UPPER;\r
}\r
else\r
{\r
- description = "To Lower Case";\r
+ description = MessageManager.getString("label.to_lower_case");\r
caseChange = ChangeCaseCommand.TO_LOWER;\r
}\r
\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- startEnd, caseChange\r
- );\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ startEnd, caseChange);\r
\r
ap.alignFrame.addHistoryItem(caseCommand);\r
\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
\r
}\r
}\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
cap.setForInput(null);\r
Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
\r
String[] omitHidden = null;\r
\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = ap.av.getViewAsString(true);\r
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens\r
+ // or we simply trust the user wants\r
+ // wysiwig behaviour\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());\r
+ omitHidden = ap.av.getViewAsString(true);\r
+ Alignment oal = new Alignment(ap.av.getSequenceSelection());\r
+ AlignmentAnnotation[] nala = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+ if (nala != null)\r
+ {\r
+ for (int i = 0; i < nala.length; i++)\r
+ {\r
+ AlignmentAnnotation na = nala[i];\r
+ oal.addAnnotation(na);\r
+ }\r
}\r
-\r
- cap.setText(new FormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- ap.av.getSelectionAsNewSequence(),\r
- omitHidden));\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
+ oal, omitHidden, csel, sg));\r
+ oal = null;\r
}\r
\r
public void pdbFromFile_actionPerformed()\r
{\r
- jalview.io.JalviewFileChooser chooser\r
- = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Select a PDB file");\r
- chooser.setToolTipText("Load a PDB file");\r
+ chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
+ chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
\r
int value = chooser.showOpenDialog(null);\r
\r
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
{\r
- PDBEntry entry = new PDBEntry();\r
String choice = chooser.getSelectedFile().getPath();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
- jalview.io.AppletFormatAdapter.FILE);\r
-\r
- if (pdbfile.id == null)\r
- {\r
- String reply = JOptionPane.showInternalInputDialog(\r
- Desktop.desktop,\r
- "Couldn't find a PDB id in the file supplied."\r
- + "Please enter an Id to identify this structure.",\r
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- entry.setId(reply);\r
- }\r
- else\r
- {\r
- entry.setId(pdbfile.id);\r
- }\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- entry.setFile(choice);\r
- sequence.getDatasetSequence().addPDBId(entry);\r
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,\r
+ jalview.io.AppletFormatAdapter.FILE, sequence, true);\r
}\r
\r
}\r
public void enterPDB_actionPerformed()\r
{\r
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
+ MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
\r
if (id != null && id.length() > 0)\r
{\r
PDBEntry entry = new PDBEntry();\r
- entry.setId(id);\r
- sequence.getDatasetSequence()\r
- .addPDBId(entry);\r
+ entry.setId(id.toUpperCase());\r
+ sequence.getDatasetSequence().addPDBId(entry);\r
}\r
}\r
\r
public void discoverPDB_actionPerformed()\r
{\r
- new jalview.io.DBRefFetcher(\r
- ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+\r
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]\r
+ { sequence }\r
+ : ap.av.getSequenceSelection());\r
+ Thread discpdb = new Thread(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+\r
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)\r
+ .fetchDBRefs(false);\r
+ }\r
+\r
+ });\r
+ discpdb.start();\r
}\r
\r
public void sequenceFeature_actionPerformed()\r
return;\r
}\r
\r
- int gSize = sg.getSize();\r
- SequenceI[] seqs = new SequenceI[gSize];\r
- SequenceFeature[] features = new SequenceFeature[gSize];\r
+ int rsize = 0, gSize = sg.getSize();\r
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
\r
for (int i = 0; i < gSize; i++)\r
{\r
- seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
int end = sg.findEndRes(sg.getSequenceAt(i));\r
- features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
+ if (start <= end)\r
+ {\r
+ seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();\r
+ features[rsize] = new SequenceFeature(null, null, null, start, end,\r
+ "Jalview");\r
+ rsize++;\r
+ }\r
}\r
-\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .amendFeatures(seqs, features, true, ap))\r
- {\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- ap.av.setShowSequenceFeatures(true);\r
+ rseqs = new SequenceI[rsize];\r
+ tfeatures = new SequenceFeature[rsize];\r
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
+ System.arraycopy(features, 0, tfeatures, 0, rsize);\r
+ features = tfeatures;\r
+ seqs = rseqs;\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
+ features, true, ap))\r
+ {\r
+ ap.alignFrame.setShowSeqFeatures(true);\r
ap.highlightSearchResults(null);\r
}\r
}\r
new TextColourChooser().chooseColour(ap, sg);\r
}\r
}\r
+\r
+ public void colourByStructure(String pdbid)\r
+ {\r
+ Annotation[] anots = ap.av.getStructureSelectionManager()\r
+ .colourSequenceFromStructure(sequence, pdbid);\r
+\r
+ AlignmentAnnotation an = new AlignmentAnnotation("Structure",\r
+ "Coloured by " + pdbid, anots);\r
+\r
+ ap.av.getAlignment().addAnnotation(an);\r
+ an.createSequenceMapping(sequence, 0, true);\r
+ // an.adjustForAlignment();\r
+ ap.av.getAlignment().setAnnotationIndex(an, 0);\r
+\r
+ ap.adjustAnnotationHeight();\r
+\r
+ sequence.addAlignmentAnnotation(an);\r
+\r
+ }\r
+\r
+ public void editSequence_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ if (sg != null)\r
+ {\r
+ if (sequence == null)\r
+ sequence = (Sequence) sg.getSequenceAt(0);\r
+\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ sequence.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
+ MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
+ EditCommand.REPLACE, dialog.getName().replace(' ',\r
+ ap.av.getGapCharacter()),\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());\r
+\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+ }\r
+ }\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff