/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * 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 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/>.
*/
package jalview.gui;
-import java.io.*;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.MutableTreeNode;
+import javax.swing.tree.TreeModel;
-import MCview.*;
import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import java.io.File;
import jalview.io.*;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.Rectangle;
import java.awt.BorderLayout;
-import java.awt.Dimension;
public class SequenceFetcher extends JPanel implements Runnable
{
final String noDbSelected = "-- Select Database --";
- Hashtable sources = new Hashtable();
-
private static jalview.ws.SequenceFetcher sfetch = null;
- private static String dasRegistry = null;
+ private static long lastDasSourceRegistry = -3;
+
+ private static DasSourceRegistryI dasRegistry = null;
+
+ private static boolean _initingFetcher = false;
+
+ private static Thread initingThread = null;
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
*
- * @param guiWindow -
- * where the initialisation delay message should be shown
+ * @param guiWindow
+ * - where the initialisation delay message should be shown
* @return the singleton instance of the sequence fetcher client
*/
public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
final IProgressIndicator guiWindow)
{
+ if (_initingFetcher && initingThread != null && initingThread.isAlive())
+ {
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ // initting happening on another thread - so wait around to see if it
+ // finishes.
+ while (_initingFetcher && initingThread != null
+ && initingThread.isAlive())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ }
if (sfetch == null
- || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (jalview.bin.Cache
+ .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ .getDasSourceRegistry().getLocalSourceString())
+ .hashCode())
{
+ _initingFetcher = true;
+ initingThread = Thread.currentThread();
/**
* give a visual indication that sequence fetcher construction is occuring
*/
guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
Thread.currentThread().hashCode());
}
- dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry.refreshSources();
+
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
Thread.currentThread().hashCode());
}
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+ .getLocalSourceString()).hashCode();
sfetch = sf;
-
+ _initingFetcher = false;
+ initingThread = null;
}
return sfetch;
}
sf.start();
}
+ private class DatabaseAuthority extends DefaultMutableTreeNode
+ {
+
+ };
+
+ private class DatabaseSource extends DefaultMutableTreeNode
+ {
+
+ };
+
/**
* called by thread spawned by constructor
*
{
alignFrame = (AlignFrame) guiWindow;
}
-
- database.addItem(noDbSelected);
- /*
- * Dynamically generated database list will need a translation function from
- * internal source to externally distinct names. UNIPROT and UP_NAME are
- * identical DB sources, and should be collapsed.
- */
-
- String dbs[] = sfetch.getOrderedSupportedSources();
- for (int i = 0; i < dbs.length; i++)
- {
- if (!sources.containsValue(dbs[i]))
- {
- String name = sfetch.getSourceProxy(dbs[i]).getDbName();
- // duplicate source names are thrown away, here.
- if (!sources.containsKey(name))
- {
- database.addItem(name);
- }
- // overwrite with latest version of the retriever for this source
- sources.put(name, dbs[i]);
- }
- }
+ database = new JDatabaseTree(sfetch);
try
{
jbInit();
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
}
}
{
this.setLayout(borderLayout2);
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ database.setFont(JvSwingUtils.getLabelFont());
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1
- .setText("Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation
+ .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ replacePunctuation.setText("Replace commas with semi-colons");
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
close_actionPerformed(e);
}
});
- textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
jPanel1.add(close);
jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
-
+ databaseButt = database.getDatabaseSelectorButton();
+ databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- dbeg.setText("Example query: " + db.getTestQuery());
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size()
+ + " others)" : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText("Example query: " + eq);
+ replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
} catch (Exception ex)
{
dbeg.setText("");
+ replacePunctuation.setEnabled(true);
}
jPanel2.repaint();
}
});
dbeg.setText("");
- jPanel2.add(database, java.awt.BorderLayout.NORTH);
+ jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
- jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+ jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
// jPanel2.setPreferredSize(new Dimension())
jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- textArea.setText(db.getTestQuery());
+ textArea.setText(database.getExampleQueries());
} catch (Exception ex)
{
}
JLabel dbeg = new JLabel();
- JComboBox database = new JComboBox();
+ JDatabaseTree database;
+
+ JButton databaseButt;
JLabel jLabel1 = new JLabel();
+ JCheckBox replacePunctuation = new JCheckBox();
+
JButton ok = new JButton();
JButton clear = new JButton();
public void run()
{
String error = "";
- if (database.getSelectedItem().equals(noDbSelected))
+ if (!database.hasSelection())
{
error += "Please select the source database\n";
}
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ // TODO: make this transformation more configurable
+ com.stevesoft.pat.Regex empty;
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ empty = new com.stevesoft.pat.Regex(
+ // replace commas and spaces with a semicolon
+ "(\\s|[,; ])+", ";");
+ }
+ else
+ {
+ // just turn spaces and semicolons into single semicolons
+ empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ }
textArea.setText(empty.replaceAll(textArea.getText()));
- if (textArea.getText().length() == 0)
+ // see if there's anthing to search with
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ .getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
resetDialog();
return;
}
- AlignmentI aresult = null;
- Object source = database.getSelectedItem();
+ ArrayList<String> aresultq = new ArrayList<String>();
+ ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+ DbSourceProxy proxy = database.getSelectedSources().get(0);
Enumeration en = new StringTokenizer(textArea.getText(), ";");
+ boolean isAliSource = false;
try
{
- guiWindow.setProgressBar("Fetching Sequences from "
- + database.getSelectedItem(), Thread.currentThread()
- .hashCode());
- DbSourceProxy proxy = sfetch.getSourceProxy(
- (String) sources.get(source));
- if (proxy.getAccessionSeparator()==null)
+ guiWindow.setProgressBar(
+ "Fetching Sequences from " + proxy.getDbName(), Thread
+ .currentThread().hashCode());
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ if (proxy.getAccessionSeparator() == null)
{
while (en.hasMoreElements())
{
String item = (String) en.nextElement();
- try {
- if (aresult!=null)
+ try
+ {
+ if (aresult != null)
{
- try {
+ try
+ {
// give the server a chance to breathe
Thread.sleep(5);
} catch (Exception e)
}
}
- AlignmentI indres = proxy.getSequenceRecords(item);
- if (indres!=null)
+
+ AlignmentI indres = null;
+ try
{
- if (aresult == null)
- {
- aresult = indres;
- } else {
- aresult.append(indres);
- }
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + item + " from "
+ + proxy.getDbName(), oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(item);
+ aresult.add(indres);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.info("Error retrieving "+item+" from "+source,e);
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + proxy.getDbName(), e);
}
}
- } else {
+ }
+ else
+ {
StringBuffer multiacc = new StringBuffer();
while (en.hasMoreElements())
{
multiacc.append(proxy.getAccessionSeparator());
}
}
- aresult = proxy
- .getSequenceRecords(multiacc.toString());
+ try
+ {
+ aresultq.add(multiacc.toString());
+ aresult.add(proxy.getSequenceRecords(multiacc.toString()));
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+
}
} catch (Exception e)
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
- if (aresult != null)
+ if (aresult != null && aresult.size() > 0)
{
- parseResult(aresult, null, null);
+ AlignmentI ar = null;
+ if (isAliSource)
+ {
+ // new window for each result
+ while (aresult.size() > 0)
+ {
+ parseResult(aresult.remove(0), aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle(), null);
+ }
+ }
+ else
+ {
+ // concatenate all results in one window
+ while (aresult.size() > 0)
+ {
+ if (ar == null)
+ {
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
+ }
+ ;
+ }
+ parseResult(ar, null, null);
+ }
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
- /*
- * result = new StringBuffer(); if
- * (database.getSelectedItem().equals("Uniprot")) {
- * getUniprotFile(textArea.getText()); } else if
- * (database.getSelectedItem().equals("EMBL") ||
- * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
- * database.getSelectedItem().equals("EMBLCDS") ?
- * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
- *
- * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
- * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch =
- * new EBIFetchClient(); String qry =
- * database.getSelectedItem().toString().toLowerCase( ) + ":" +
- * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
- *
- * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
- * reply.exists()) { efile =
- * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null) {
- * for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
- * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
- * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
- * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
- * SequenceI[seqparts.length]; } else { newseqs = new
- * SequenceI[seqs.length+seqparts.length];
- *
- * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
- * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
- * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
- * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
- * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
- * null)!=null) { result.append("# Successfully parsed the
- * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
- * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
- * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
- * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
- * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
- * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
- * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
- * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int j=0;j<seqparts.length;
- * i++, j++) { newseqs[i] = seqparts[j]; } seqs=newseqs; } result.append("#
- * Success for "+query.toUpperCase()+"\n"); } } if (seqs != null &&
- * seqs.length > 0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
- * result.append( "# Successfully parsed the PDB File Queries into an
- * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
- * try { result.append(new FastaFile(
- * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
- * textArea.getText().toUpperCase(), "URL").print() );
- *
- * if(result.length()>0) { parseResult( result.toString(),
- * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
- * result = null; } }
- *
- * if (result == null || result.length() == 0) { showErrorMessage("Error
- * retrieving " + textArea.getText() + " from " + database.getSelectedItem()); }
- *
- * resetDialog(); return; }
- *
- * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
- * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
- *
- * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
- * dbref.getUniprotEntries(file);
- *
- * if (entries != null) { //First, make the new sequences Enumeration en =
- * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
- * (UniprotEntry) en.nextElement();
- *
- * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
- * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); } en2 =
- * entry.getName().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); }
- *
- * if (entry.getProtein() != null) { name.append(" " +
- * entry.getProtein().getName().elementAt(0)); }
- *
- * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- * "\n"); }
- *
- * //Then read in the features and apply them to the dataset Alignment al =
- * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
- * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
- * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
- * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
- *
- * onlyPdbEntries.addElement(pdb); }
- *
- * Enumeration en2 = entry.getAccession().elements(); while
- * (en2.hasMoreElements()) {
- * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
- *
- *
- *
- *
- * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
- * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
- * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
- * e.nextElement(); sf.setFeatureGroup("Uniprot");
- * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } } }
- *
- * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
- * chain = null; if (id.indexOf(":") > -1) { chain =
- * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
- *
- * EBIFetchClient ebi = new EBIFetchClient(); String file =
- * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file ==
- * null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
- * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
- * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
- * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
- * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
- * Sequence - who's dataset includes any special features added from the PDB
- * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
- * PDB chain sequences retrieved from the PDB
- * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
- * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
- * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
- * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
- * DBRefEtntry because we have obtained the PDB file from a verifiable source //
- * JBPNote - PDB DBRefEntry should also carry the chain and mapping
- * information DBRefEntry dbentry = new
- * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
- * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
- * result.addElement(sq.deriveSequence()); } }
- *
- * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
- * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file {
- * jalview.bin.Cache.log.warn("Exception when retrieving " +
- * textArea.getText() + " from " + database.getSelectedItem(), ex); return
- * null; }
- *
- *
- * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
- * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
- * result.setElementAt(null,i); } return results; }
- */
AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
return null;
}
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
+ */
+ public String getDefaultRetrievalTitle()
+ {
+ return "Retrieved from " + database.getSelectedItem();
+ }
+
AlignmentI parseResult(AlignmentI al, String title,
String currentFileFormat)
{
if (title == null)
{
- title = "Retrieved from " + database.getSelectedItem();
+ title = getDefaultRetrievalTitle();
}
- SequenceFeature[] sfs=null;
- for (Enumeration sq=al.getSequences().elements(); sq.hasMoreElements();)
+ SequenceFeature[] sfs = null;
+ for (Enumeration sq = al.getSequences().elements(); sq
+ .hasMoreElements();)
{
- if ((sfs=((SequenceI)sq.nextElement()).getDatasetSequence().getSequenceFeatures())!=null)
+ if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
+ .getSequenceFeatures()) != null)
{
- if (sfs.length>0)
+ if (sfs.length > 0)
{
af.setShowSeqFeatures(true);
break;
}
}
-
+
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
+ alignFrame.viewport.getAlignment().addSequence(
+ al.getSequenceAt(i)); // this
// also
// creates
// dataset
// sequence
// entries
}
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
.getHeight());
- alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.getAlignment().getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
alignFrame.viewport.getAlignment().getSequences());
}
git://source.jalview.org / jalview.git / blobdiff