/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
+import java.io.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.io.EBIFetchClient;\r
+import javax.swing.*;\r
+\r
import MCview.*;\r
import jalview.datamodel.*;\r
-import jalview.analysis.AlignSeq;\r
+import jalview.datamodel.xdb.embl.*;\r
import java.io.File;\r
import jalview.io.*;\r
-import java.util.*;\r
-\r
+import java.awt.Rectangle;\r
+import java.awt.BorderLayout;\r
+import java.awt.Dimension;\r
\r
public class SequenceFetcher\r
- extends JPanel implements Runnable\r
+extends JPanel implements Runnable\r
{\r
JInternalFrame frame;\r
AlignFrame alignFrame;\r
StringBuffer result;\r
+ final String noDbSelected = "-- Select Database --";\r
public SequenceFetcher(AlignFrame af)\r
{\r
alignFrame = af;\r
- database.addItem("-- Select Database --");\r
+ database.addItem(noDbSelected);\r
database.addItem("Uniprot");\r
database.addItem("EMBL");\r
database.addItem("EMBLCDS");\r
database.addItem("PDB");\r
+ database.addItem("PFAM");\r
\r
try\r
{\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
+ }\r
else\r
- Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 125);\r
+ {\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
+ }\r
+ }\r
+\r
+ private String getFrameTitle()\r
+ {\r
+ return ( (alignFrame == null) ? "New " : "Additional ") +\r
+ "Sequence Fetcher";\r
}\r
\r
private void jbInit()\r
- throws Exception\r
+ throws Exception\r
{\r
- this.setLayout(gridBagLayout1);\r
+ this.setLayout(borderLayout2);\r
\r
database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- database.setMinimumSize(new Dimension(160, 21));\r
- database.setPreferredSize(new Dimension(160, 21));\r
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
jLabel1.setText(\r
- "Separate multiple accession ids with semi colon \";\"");\r
+ "Separate multiple accession ids with semi colon \";\"");\r
ok.setText("OK");\r
ok.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- ok_actionPerformed(e);\r
+ ok_actionPerformed();\r
}\r
});\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
+ close.setText("Close");\r
+ close.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- cancel_actionPerformed(e);\r
+ close_actionPerformed(e);\r
}\r
});\r
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- textfield.addActionListener(new ActionListener()\r
+ textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ textArea.setLineWrap(true);\r
+ textArea.addKeyListener(new KeyAdapter()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void keyPressed(KeyEvent e)\r
{\r
- ok_actionPerformed(e);\r
+ System.out.println(e.getKeyCode()+" "+KeyEvent.VK_ENTER);\r
+ if(e.getKeyCode()==KeyEvent.VK_ENTER)\r
+ ok_actionPerformed();\r
}\r
});\r
+ jPanel3.setLayout(borderLayout1);\r
+ borderLayout1.setVgap(5);\r
jPanel1.add(ok);\r
- jPanel1.add(cancel);\r
- this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(7, 4, 0, 6), 77, 6));\r
- this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.BOTH,\r
- new Insets(7, -2, 7, 12), 241, -2));\r
- this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(0, 4, 0, 0), 1, 0));\r
- this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.CENTER,\r
- GridBagConstraints.HORIZONTAL,\r
- new Insets(0, 0, 0, 6), 200, 1));\r
+ jPanel1.add(close);\r
+ jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);\r
+ jPanel2.add(database);\r
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);\r
+ jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
+ jScrollPane1.getViewport().add(textArea);\r
+\r
}\r
\r
JComboBox database = new JComboBox();\r
JLabel jLabel1 = new JLabel();\r
JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
+ JButton close = new JButton();\r
JPanel jPanel1 = new JPanel();\r
- JTextField textfield = new JTextField();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void cancel_actionPerformed(ActionEvent e)\r
+ JTextArea textArea = new JTextArea();\r
+ JScrollPane jScrollPane1 = new JScrollPane();\r
+ JPanel jPanel2 = new JPanel();\r
+ JPanel jPanel3 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ public void close_actionPerformed(ActionEvent e)\r
{\r
try\r
{\r
{}\r
}\r
\r
- public void ok_actionPerformed(ActionEvent e)\r
+ public void ok_actionPerformed()\r
{\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
database.setEnabled(false);\r
- textfield.setEnabled(false);\r
+ textArea.setEnabled(false);\r
ok.setEnabled(false);\r
- cancel.setEnabled(false);\r
+ close.setEnabled(false);\r
\r
Thread worker = new Thread(this);\r
worker.start();\r
}\r
\r
+ private void resetDialog()\r
+ {\r
+ database.setEnabled(true);\r
+ textArea.setEnabled(true);\r
+ ok.setEnabled(true);\r
+ close.setEnabled(true);\r
+ }\r
+\r
public void run()\r
{\r
- result = new StringBuffer();\r
+ String error = "";\r
+ if (database.getSelectedItem().equals(noDbSelected))\r
+ {\r
+ error += "Please select the source database\n";\r
+ }\r
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
+ textArea.setText(empty.replaceAll(textArea.getText()));\r
+ if (textArea.getText().length() == 0)\r
+ {\r
+ error += "Please enter a (semi-colon separated list of) database id(s)";\r
+ }\r
+ if (error.length() > 0)\r
+ {\r
+ showErrorMessage(error);\r
+ resetDialog();\r
+ return;\r
+ }\r
+\r
+ result = new StringBuffer();\r
if (database.getSelectedItem().equals("Uniprot"))\r
{\r
- getUniprotFile(textfield.getText());\r
+ getUniprotFile(textArea.getText());\r
}\r
else if (database.getSelectedItem().equals("EMBL")\r
|| database.getSelectedItem().equals("EMBLCDS"))\r
{\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- String[] reply = dbFetch.fetchData(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + textfield.getText(),\r
- "fasta", "raw");\r
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")\r
+ ? jalview.datamodel.DBRefSource.EMBLCDS\r
+ : jalview.datamodel.DBRefSource.EMBL;\r
+\r
+ StringTokenizer st = new StringTokenizer(textArea.getText(), ";");\r
+ SequenceI[] seqs = null;\r
+ while(st.hasMoreTokens())\r
+ {\r
+ EBIFetchClient dbFetch = new EBIFetchClient();\r
\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
+ File reply = dbFetch.fetchDataAsFile(\r
+ database.getSelectedItem().toString().toLowerCase(\r
+ ) + ":" + st.nextToken(),\r
+ "emblxml",null);\r
\r
- parseResult(result.toString());\r
+ jalview.datamodel.xdb.embl.EmblFile efile=null;\r
+ if (reply != null && reply.exists())\r
+ {\r
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
+ }\r
+ if (efile!=null) {\r
+ for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {\r
+ EmblEntry entry = (EmblEntry) i.next();\r
+ SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);\r
+ if (seqparts!=null) {\r
+ SequenceI[] newseqs = null;\r
+ int si=0;\r
+ if (seqs==null) {\r
+ newseqs = new SequenceI[seqparts.length];\r
+ } else {\r
+ newseqs = new SequenceI[seqs.length+seqparts.length];\r
+\r
+ for (;si<seqs.length; si++) {\r
+ newseqs[si] = seqs[si];\r
+ seqs[si] = null;\r
+ }\r
+ }\r
+ for (int j=0;j<seqparts.length; si++, j++) {\r
+ newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer\r
+ }\r
+ seqs=newseqs;\r
+\r
+ }\r
+ }\r
+ } else {\r
+ result=null;\r
+ }\r
+ }\r
+ if (seqs!=null && seqs.length>0) {\r
+ if (parseResult(new Alignment(seqs), null, null)!=null)\r
+ result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");\r
+ }\r
}\r
else if (database.getSelectedItem().equals("PDB"))\r
{\r
- result = getPDBFile(textfield.getText().toUpperCase());\r
- parseResult(result.toString());\r
+ StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");\r
+ String query;\r
+ SequenceI[] seqs = null;\r
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
+ {\r
+ SequenceI[] seqparts = getPDBFile(query.toUpperCase());\r
+ if (seqparts != null)\r
+ {\r
+ if (seqs == null)\r
+ {\r
+ seqs = seqparts;\r
+ }\r
+ else\r
+ {\r
+ SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];\r
+ int i=0;\r
+ for (; i < seqs.length; i++)\r
+ {\r
+ newseqs[i] = seqs[i];\r
+ seqs[i] = null;\r
+ }\r
+ for (int j=0;j<seqparts.length; i++, j++)\r
+ {\r
+ newseqs[i] = seqparts[j];\r
+ }\r
+ seqs=newseqs;\r
+ }\r
+ result.append("# Success for "+query.toUpperCase()+"\n");\r
+ }\r
+ }\r
+ if (seqs != null && seqs.length > 0)\r
+ {\r
+ if (parseResult(new Alignment(seqs), null, null)!=null)\r
+ {\r
+ result.append(\r
+ "# Successfully parsed the PDB File Queries into an Alignment");\r
+ }\r
+ }\r
}\r
+ else if( database.getSelectedItem().equals("PFAM"))\r
+ {\r
+ try\r
+ {\r
+ result.append(new FastaFile(\r
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
+ + textArea.getText().toUpperCase(), "URL").print()\r
+ );\r
\r
+ if(result.length()>0)\r
+ {\r
+ parseResult( result.toString(), textArea.getText().toUpperCase() );\r
+ }\r
\r
- if (result == null || result.length() == 0)\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ result = null;\r
+ }\r
+ }\r
\r
+ if (result == null || result.length() == 0)\r
+ {\r
+ showErrorMessage("Error retrieving " + textArea.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\r
\r
- database.setEnabled(true);\r
- textfield.setEnabled(true);\r
- ok.setEnabled(true);\r
- cancel.setEnabled(true);\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
+ resetDialog();\r
+ return;\r
}\r
\r
void getUniprotFile(String id)\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
- Vector entries = sff.getUniprotEntries(file);\r
+ File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+\r
+ DBRefFetcher dbref = new DBRefFetcher();\r
+ Vector entries = dbref.getUniprotEntries(file);\r
\r
- if(entries!=null)\r
+ if (entries != null)\r
{\r
//First, make the new sequences\r
Enumeration en = entries.elements();\r
while (en.hasMoreElements())\r
{\r
UniprotEntry entry = (UniprotEntry) en.nextElement();\r
- StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
+\r
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
Enumeration en2 = entry.getAccession().elements();\r
- while(en2.hasMoreElements())\r
+ while (en2.hasMoreElements())\r
{\r
name.append("|");\r
name.append(en2.nextElement());\r
}\r
en2 = entry.getName().elements();\r
- while(en2.hasMoreElements())\r
+ while (en2.hasMoreElements())\r
{\r
name.append("|");\r
name.append(en2.nextElement());\r
}\r
\r
- if(entry.getProteinName()!=null)\r
- name.append(" "+entry.getProteinName().elementAt(0));\r
+ if (entry.getProtein() != null)\r
+ {\r
+ name.append(" " + entry.getProtein().getName().elementAt(0));\r
+ }\r
\r
- result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
+ result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
+ "\n");\r
\r
}\r
\r
//Then read in the features and apply them to the dataset\r
- SequenceI [] sequence = parseResult(result.toString());\r
- for(int i=0; i<entries.size(); i++)\r
+ Alignment al = parseResult(result.toString(), null);\r
+ for (int i = 0; i < entries.size(); i++)\r
{\r
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
Enumeration e = entry.getDbReference().elements();\r
{\r
PDBEntry pdb = (PDBEntry) e.nextElement();\r
if (!pdb.getType().equals("PDB"))\r
+ {\r
continue;\r
+ }\r
\r
onlyPdbEntries.addElement(pdb);\r
}\r
\r
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
+ Enumeration en2 = entry.getAccession().elements();\r
+ while (en2.hasMoreElements())\r
+ {\r
+ al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(\r
+ DBRefSource.UNIPROT,\r
+ "0",\r
+ en2.nextElement().toString()));\r
+ }\r
+\r
+\r
+\r
\r
+ al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);\r
+ if (entry.getFeature() != null)\r
+ {\r
+ e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setFeatureGroup("Uniprot");\r
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );\r
+ }\r
+ }\r
}\r
}\r
}\r
\r
- StringBuffer getPDBFile(String id)\r
+ SequenceI[] getPDBFile(String id)\r
+ {\r
+ Vector result = new Vector();\r
+ String chain = null;\r
+ if (id.indexOf(":") > -1)\r
{\r
- StringBuffer result = new StringBuffer();\r
- String chain = null;\r
- if (id.indexOf(":") > -1)\r
- {\r
- chain = id.substring(id.indexOf(":") + 1);\r
- id = id.substring(0, id.indexOf(":"));\r
- }\r
+ chain = id.substring(id.indexOf(":") + 1);\r
+ id = id.substring(0, id.indexOf(":"));\r
+ }\r
\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- try\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").\r
+ getAbsolutePath();\r
+ if (file == null)\r
+ {\r
+ return null;\r
+ }\r
+ try\r
+ {\r
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);\r
+ for (int i = 0; i < pdbfile.chains.size(); i++)\r
{\r
- PDBfile pdbfile = new PDBfile(reply);\r
- for (int i = 0; i < pdbfile.chains.size(); i++)\r
+ if (chain == null ||\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
+ toUpperCase().equals(chain))\r
{\r
- if (chain == null ||\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
- toUpperCase().equals(chain))\r
- result.append("\n>PDB|" + id + "|" +\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
- getName() +\r
- "\n"\r
- +\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
- getSequence());\r
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);\r
+ // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file\r
+ SequenceI sq = pdbchain.sequence;\r
+ // Specially formatted name for the PDB chain sequences retrieved from the PDB\r
+ sq.setName("PDB|"+id+"|"+sq.getName());\r
+ // Might need to add more metadata to the PDBEntry object\r
+ // like below\r
+ /*\r
+ * PDBEntry entry = new PDBEntry();\r
+ // Construct the PDBEntry\r
+ entry.setId(id);\r
+ if (entry.getProperty() == null)\r
+ entry.setProperty(new Hashtable());\r
+ entry.getProperty().put("chains",\r
+ pdbchain.id\r
+ + "=" + sq.getStart()\r
+ + "-" + sq.getEnd());\r
+ sq.getDatasetSequence().addPDBId(entry);\r
+ */\r
+ // Add PDB DB Refs\r
+ // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
+ DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,\r
+ "0", id + pdbchain.id);\r
+ sq.addDBRef(dbentry);\r
+ // and add seuqence to the retrieved set\r
+ result.addElement(sq.deriveSequence());\r
}\r
}\r
- catch (Exception ex) // Problem parsing PDB file\r
+\r
+ if (result.size() < 1)\r
{\r
- showErrorMessage("Error retrieving " + textfield.getText() + " from " +\r
- database.getSelectedItem());\r
- return null;\r
+ throw new Exception("WsDBFetch for PDB id resulted in zero result size");\r
}\r
+ }\r
+ catch (Exception ex) // Problem parsing PDB file\r
+ {\r
+ jalview.bin.Cache.log.warn("Exception when retrieving " +\r
+ textArea.getText() + " from " +\r
+ database.getSelectedItem(), ex);\r
+ return null;\r
+ }\r
+\r
\r
- return result;\r
+ SequenceI[] results = new SequenceI[result.size()];\r
+ for (int i = 0, j = result.size(); i < j; i++)\r
+ {\r
+ results[i] = (SequenceI) result.elementAt(i);\r
+ result.setElementAt(null,i);\r
}\r
+ return results;\r
+ }\r
+ Alignment parseResult(String result, String title)\r
+ {\r
+ String format = new IdentifyFile().Identify(result, "Paste");\r
+ Alignment sequences = null;\r
+ if (FormatAdapter.isValidFormat(format))\r
+ {\r
+ sequences = null;\r
+ try\r
+ {\r
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
+ format);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
\r
- SequenceI[] parseResult(String result)\r
+ if (sequences!=null)\r
+ {\r
+ return parseResult(sequences, title, format);\r
+ }\r
+ }\r
+ else\r
{\r
- String format = IdentifyFile.Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
+ showErrorMessage("Error retrieving " + textArea.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\r
\r
- if (FormatAdapter.formats.contains(format))\r
+ return null;\r
+ }\r
+\r
+ Alignment parseResult(Alignment al, String title, String currentFileFormat)\r
+ {\r
+\r
+ if (al != null && al.getHeight() > 0)\r
+ {\r
+ if (alignFrame == null)\r
{\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
- if (sequences != null && sequences.length>0)\r
+ AlignFrame af = new AlignFrame(al,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ if (currentFileFormat!=null)\r
{\r
- if(alignFrame==null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- else\r
- {\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- alignFrame.viewport.alignment.addSequence(sequences[i]);\r
-\r
- ////////////////////////////\r
- //Datset needs extension;\r
- /////////////////////////////\r
- Sequence ds = new Sequence(sequences[i].getName(),\r
- AlignSeq.extractGaps("-. ",\r
- sequences[i].getSequence()),\r
- sequences[i].getStart(),\r
- sequences[i].getEnd());\r
- sequences[i].setDatasetSequence(ds);\r
- alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
- }\r
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
- getHeight());\r
- alignFrame.viewport.alignment.getWidth();\r
- alignFrame.viewport.firePropertyChange("alignment", null,\r
- alignFrame.viewport.getAlignment().getSequences());\r
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?\r
+ }\r
\r
- }\r
+ if(title==null)\r
+ {\r
+ title = "Retrieved from " + database.getSelectedItem();\r
+ }\r
\r
- if (database.getSelectedItem().equals("PDB"))\r
- {\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(textfield.getText());\r
- sequences[i].getDatasetSequence().addPDBId(entry);\r
- }\r
- }\r
+ Desktop.addInternalFrame(af,\r
+ title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
\r
+ try\r
+ {\r
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
}\r
- else\r
- showErrorMessage( "Error retrieving "+textfield.getText()\r
- +" from "+database.getSelectedItem());\r
+ catch (Exception ex)\r
+ {}\r
}\r
-\r
- return sequences;\r
-\r
+ else\r
+ {\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries\r
+ }\r
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
+ getHeight());\r
+ alignFrame.viewport.alignment.getWidth();\r
+ alignFrame.viewport.firePropertyChange("alignment", null,\r
+ alignFrame.viewport.\r
+ getAlignment().getSequences());\r
+ }\r
+ }\r
+ return al;\r
}\r
\r
- void showErrorMessage(String error)\r
+ void showErrorMessage(final String error)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
+ resetDialog();\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "Error Retrieving Data",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
}\r
\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff