import java.util.*;\r
import java.io.InputStreamReader;\r
import java.io.BufferedReader;\r
+import java.io.FileReader;\r
\r
public class AlignFrame\r
extends GAlignFrame\r
\r
}\r
\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseGroupsFile(String file)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq = null;\r
+ String line, text, token;\r
+ UserColourScheme ucs;\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceGroup sg;\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() != 6)\r
+ {\r
+ System.out.println("Groups file " + file +\r
+ " is invalid. Read help file.\nLine: \n"\r
+ +lineNo +": "+line);\r
+ break;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ text = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+ ucs = new UserColourScheme(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ sg.addSequence(seq, false);\r
+\r
+ viewport.alignment.addGroup(sg);\r
+\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
jalview.bin.JalviewLite.addFrame(frame,\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
viewport.getAlignment().\r
getSequences()));\r
}\r
SequenceI[] sequences = null;\r
\r
String format = IdentifyFile.Identify(text, "Paste");\r
- sequences = new FormatAdapter().readFile(text, "Paste", format);\r
+ sequences = new AppletFormatAdapter().readFile(text, "Paste", format);\r
\r
if (sequences != null)\r
{\r
while (e.hasMoreElements())\r
{\r
SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() > seq.getEnd())\r
+ if (sf.getBegin() > seq.getEnd())\r
{\r
continue;\r
}\r
\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fstart = seq.findIndex(sf.getBegin()) - 1;\r
int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
if ( (fstart <= end && fend >= start))\r
while (e.hasMoreElements())\r
{\r
SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
+ if (sf.getBegin() <= sequence.findPosition(res) &&\r
sf.getEnd() >= sequence.findPosition(res))\r
{\r
if (sbuffer.length() > 0)\r
if (file != null)\r
{\r
add(launcher);\r
- file = applet.getCodeBase() + file;\r
+ if(!file.startsWith("http://") && !file.startsWith("file://"))\r
+ file = applet.getCodeBase() + file;\r
+\r
launcher.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
\r
\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
- SequenceI[] sequences = new FormatAdapter().readFile(args[0], "File", format);\r
+ SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
\r
if ( (sequences != null) && (sequences.length > 0))\r
{\r
public void run()\r
{\r
SequenceI[] sequences = null;\r
- sequences = new FormatAdapter().readFile(file, protocol, format);\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
\r
if ((sequences != null) && (sequences.length > 0))\r
{\r
*/\r
public class Alignment implements AlignmentI\r
{\r
+ protected Alignment dataset;\r
protected Vector sequences;\r
protected Vector groups = new Vector();\r
protected Vector superGroup = new Vector();\r
protected char gapCharacter = '-';\r
- protected boolean isNucleotide = true;\r
-\r
+ protected Provenance provenance;\r
+ protected int type = NUCLEOTIDE;\r
+ public static final int PROTEIN = 0;\r
+ public static final int NUCLEOTIDE = 1;\r
\r
/** DOCUMENT ME!! */\r
public AlignmentAnnotation[] annotations;\r
*/\r
public Alignment(SequenceI[] seqs)\r
{\r
- int i=0, iSize = seqs.length, j, jSize;\r
- while(isNucleotide && i<iSize)\r
- {\r
- jSize = seqs[i].getLength();\r
- for(j=0; j<jSize; j++)\r
- {\r
- if(!jalview.schemes.ResidueProperties.nucleotideHash.containsKey(seqs[i].getSequence(j, j+1))\r
- && !jalview.util.Comparison.isGap(seqs[i].getSequence().charAt(j)))\r
- {\r
- isNucleotide = false;\r
- break;\r
- }\r
- }\r
- i++;\r
- }\r
+ int i=0;\r
+\r
+ if( jalview.util.Comparison.isNucleotide(seqs))\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
\r
sequences = new Vector();\r
\r
aSize = annotations.length + 1;\r
}\r
\r
+\r
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
int i = 0;\r
\r
\r
public void setNucleotide(boolean b)\r
{\r
- isNucleotide = b;\r
+ if(b)\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
}\r
\r
public boolean isNucleotide()\r
{\r
- return isNucleotide;\r
+ if(type==NUCLEOTIDE)\r
+ return true;\r
+ else\r
+ return false;\r
+ }\r
+\r
+ public void setDataset(Alignment data)\r
+ {\r
+ if(dataset==null && data==null)\r
+ {\r
+ // Create a new dataset for this alignment.\r
+ // Can only be done once, if dataset is not null\r
+ // This will not be performed\r
+ Sequence[] seqs = new Sequence[getHeight()];\r
+ for (int i = 0; i < getHeight(); i++)\r
+ {\r
+\r
+ seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+ AlignSeq.extractGaps(\r
+ jalview.util.Comparison.GapChars,\r
+ getSequenceAt(i).getSequence()\r
+ ),\r
+ getSequenceAt(i).getStart(),\r
+ getSequenceAt(i).getEnd());\r
+ }\r
+\r
+ dataset = new Alignment(seqs);\r
+ }\r
+ else if(dataset==null && data!=null)\r
+ {\r
+ dataset = data;\r
+ }\r
+ }\r
+\r
+ public Alignment getDataset()\r
+ {\r
+ return dataset;\r
+ }\r
+\r
+ public void setProvenance(Provenance prov)\r
+ {\r
+ provenance = prov;\r
+ }\r
+ public Provenance getProvenance()\r
+ {\r
+ return provenance;\r
}\r
}\r
*/\r
public void setNucleotide(boolean b);\r
\r
+\r
+ public Alignment getDataset();\r
+\r
+ public void setDataset(Alignment dataset);\r
+\r
+ public Provenance getProvenance();\r
+\r
+ public void setProvenance(Provenance prov);\r
+\r
}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class DBRefEntry\r
+{\r
+ String source, version, accessionId;\r
+\r
+ public DBRefEntry(String source, String version, String accessionId)\r
+ {\r
+ this.source = source;\r
+ this.version = version;\r
+ this.accessionId = accessionId;\r
+ }\r
+\r
+ public String getSource()\r
+ { return source; }\r
+\r
+ public String getVersion()\r
+ { return version; }\r
+\r
+ public String getAccessionId()\r
+ { return accessionId; }\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+import java.util.*;\r
+\r
+public class Provenance\r
+{\r
+ Vector entries = new Vector();\r
+ public Provenance()\r
+ {\r
+\r
+ }\r
+\r
+ public ProvenanceEntry[] getEntries()\r
+ {\r
+ ProvenanceEntry [] ret = new ProvenanceEntry[entries.size()];\r
+ for(int i=0; i<entries.size(); i++)\r
+ ret[i] = (ProvenanceEntry)entries.elementAt(i);\r
+ return ret;\r
+ }\r
+\r
+ public void addEntry(String user, String action, java.util.Date date, String id)\r
+ {\r
+ entries.addElement( new ProvenanceEntry(user,action,date,id));\r
+ }\r
+\r
+}\r
+\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class ProvenanceEntry\r
+{\r
+ String user, action, id;\r
+ java.util.Date date;\r
+ public ProvenanceEntry(String u, String a, java.util.Date d, String i)\r
+ {\r
+ user = u; action = a; date = d; id = i;\r
+ }\r
+\r
+ public String getUser()\r
+ {return user;}\r
+\r
+ public String getAction()\r
+ {return action;}\r
+\r
+ public java.util.Date getDate()\r
+ {return date;}\r
+\r
+ public String getID()\r
+ {return id;}\r
+}\r
protected String displayId;\r
protected Color color = Color.white;\r
String pdbId;\r
+ String vamsasId;\r
+ Vector dbrefs;\r
+\r
\r
/** DOCUMENT ME!! */\r
public Vector sequenceFeatures = new Vector();\r
this.start = start;\r
this.end = end;\r
\r
+ checkValidRange();\r
+\r
+ setDisplayId();\r
+ }\r
+\r
+ void checkValidRange()\r
+ {\r
if (end < 1)\r
{\r
int endRes = 0;\r
this.end = endRes;\r
}\r
\r
- setDisplayId();\r
+ setDisplayId();\r
}\r
\r
/**\r
sequenceFeatures = v;\r
}\r
\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ sequenceFeatures = new Vector();\r
+\r
+ sequenceFeatures.addElement(sf);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
public void setSequence(String seq)\r
{\r
this.sequence = seq;\r
+ checkValidRange();\r
}\r
\r
/**\r
{\r
return color;\r
}\r
+\r
+ public String getVamsasId()\r
+ {\r
+ return vamsasId;\r
+ }\r
+\r
+ public void setVamsasId(String id)\r
+ {\r
+ vamsasId = id;\r
+ }\r
+\r
+ public Vector getDBRef()\r
+ {\r
+ return dbrefs;\r
+ }\r
+\r
+ public void addDBRef(DBRefEntry entry)\r
+ {\r
+ if(dbrefs == null)\r
+ dbrefs = new Vector();\r
+\r
+ dbrefs.addElement(entry);\r
+ }\r
+\r
}\r
*/\r
public class SequenceFeature\r
{\r
+ int position;\r
int begin;\r
int end;\r
String type;\r
String description;\r
String status;\r
\r
- /**\r
- * Creates a new SequenceFeature object.\r
- */\r
public SequenceFeature()\r
+ {}\r
+\r
+ public SequenceFeature(String type, String desc, String status, int begin, int end)\r
{\r
+ this.type = type;\r
+ this.description = desc;\r
+ this.status = status;\r
+ this.position = begin;\r
+ this.begin = begin;\r
+ this.end = end;\r
}\r
\r
- /**\r
- * Creates a new SequenceFeature object.\r
- *\r
- * @param type DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param description DOCUMENT ME!\r
- * @param status DOCUMENT ME!\r
- */\r
- public SequenceFeature(String type, int start, int end, String description,\r
- String status)\r
+ public int getPosition()\r
{\r
- this.type = type;\r
- this.begin = start;\r
- this.end = end;\r
- this.description = description;\r
- this.status = status;\r
+ return position;\r
}\r
\r
+ public void setPosition(int pos)\r
+ {\r
+ position = pos;\r
+ begin = pos;\r
+ end = pos;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getStart()\r
+ public int getBegin()\r
{\r
return begin;\r
}\r
\r
+ public void setBegin(int start)\r
+ {\r
+ this.begin = start;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return end;\r
}\r
\r
+ public void setEnd(int end)\r
+ {\r
+ this.end = end;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return type;\r
}\r
\r
+ public void setType(String type)\r
+ {\r
+ this.type = type;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return description;\r
}\r
\r
+ public void setDescription(String desc)\r
+ {\r
+ description = desc;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return status;\r
}\r
\r
- /*\r
- <xs:enumeration value="active site" />\r
- <xs:enumeration value="binding site" />\r
- <xs:enumeration value="calcium-binding region" />\r
- <xs:enumeration value="chain" />\r
- <xs:enumeration value="cross-link" />\r
- <xs:enumeration value="disulfide bond" />\r
- <xs:enumeration value="DNA-binding region" />\r
- <xs:enumeration value="domain" />\r
- <xs:enumeration value="glycosylation site" />\r
- <xs:enumeration value="helix" />\r
- <xs:enumeration value="initiator methionine" />\r
- <xs:enumeration value="lipid moiety-binding region" />\r
- <xs:enumeration value="metal ion-binding site" />\r
- <xs:enumeration value="modified residue" />\r
- <xs:enumeration value="mutagenesis site" />\r
- <xs:enumeration value="non-consecutive residues" />\r
- <xs:enumeration value="non-terminal residue" />\r
- <xs:enumeration value="nucleotide phosphate-binding region" />\r
- <xs:enumeration value="peptide" />\r
- <xs:enumeration value="propeptide" />\r
- <xs:enumeration value="repeat" />\r
- <xs:enumeration value="selenocysteine" />\r
- <xs:enumeration value="sequence conflict" />\r
- <xs:enumeration value="sequence variant" />\r
- <xs:enumeration value="signal peptide" />\r
- <xs:enumeration value="similar" />\r
- <xs:enumeration value="site" />\r
- <xs:enumeration value="splice variant" />\r
- <xs:enumeration value="strand" />\r
- <xs:enumeration value="thioether bond" />\r
- <xs:enumeration value="thiolester bond" />\r
- <xs:enumeration value="transit peptide" />\r
- <xs:enumeration value="transmembrane region" />\r
- <xs:enumeration value="turn" />\r
- <xs:enumeration value="unsure residue" />\r
- <xs:enumeration value="zinc finger region" />\r
- */\r
+ public void setStatus(String status)\r
+ {\r
+ this.status = status;\r
+ }\r
+\r
}\r
* @return DOCUMENT ME!\r
*/\r
public String getPDBId();\r
+\r
+ public String getVamsasId();\r
+\r
+ public void setVamsasId(String id);\r
+\r
+ public Vector getDBRef();\r
+\r
+ public void addDBRef(DBRefEntry entry);\r
+\r
+ public void addSequenceFeature(SequenceFeature sf);\r
}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+import java.util.Vector;\r
+\r
+public class UniprotEntry\r
+{\r
+\r
+ UniprotSequence sequence;\r
+ String name;\r
+ String accession;\r
+ Vector features;\r
+\r
+ public void setFeatures(Vector items)\r
+ {\r
+ features = items;\r
+ }\r
+\r
+ public Vector getFeatures() {\r
+ return features;\r
+ }\r
+\r
+ public void setAccession(String acc)\r
+ {\r
+ accession = acc;\r
+ }\r
+\r
+ public String getAccession()\r
+ {\r
+ return accession;\r
+ }\r
+\r
+\r
+ public void setName(String na)\r
+ {\r
+ name = na;\r
+ }\r
+ public String getName()\r
+ {\r
+ return name;\r
+ }\r
+\r
+ public UniprotSequence getUniprotSequence()\r
+ {\r
+ return sequence;\r
+ }\r
+\r
+ public void setUniprotSequence(UniprotSequence seq)\r
+ {\r
+ sequence = seq;\r
+ }\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+import java.util.Vector;\r
+\r
+public class UniprotFile\r
+{\r
+ Vector _items;\r
+\r
+ public void setUniprotEntries(Vector items) {\r
+ _items = items;\r
+ }\r
+\r
+ public Vector getUniprotEntries() {\r
+ return _items;\r
+ }\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class UniprotSequence\r
+{\r
+ /**\r
+ * internal content storage\r
+ */\r
+ private java.lang.String _content = "";\r
+\r
+ public void setContent(String seq)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int i=0; i<seq.length(); i++)\r
+ if(seq.charAt(i)!=' ')\r
+ {\r
+ sb.append(seq.charAt(i));\r
+ }\r
+ _content = sb.toString();\r
+ }\r
+\r
+ public String getContent()\r
+ { return _content; }\r
+\r
+}\r
\r
/** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_HEIGHT = 500;\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
+ AlignmentPanel alignPanel;\r
+ AlignViewport viewport;\r
+\r
+ Vector viewports = new Vector();\r
+ Vector alignPanels = new Vector();\r
\r
/** DOCUMENT ME!! */\r
public String currentFileFormat = null;\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
+ viewports.add(viewport);\r
+\r
\r
if(viewport.vconsensus==null)\r
{\r
- //Out of memory caluclating consensus.\r
+ //Out of memory calculating consensus.\r
BLOSUM62Colour.setEnabled(false);\r
PIDColour.setEnabled(false);\r
conservationMenuItem.setEnabled(false);\r
}\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
- annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
- getPreferredSize());\r
- alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
+ alignPanels.add(alignPanel);\r
\r
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
else if(sortby.equals("Pairwise Identity"))\r
sortPairwiseMenuItem_actionPerformed(null);\r
\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+ tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ if(al.getDataset()==null)\r
+ {\r
+ al.setDataset(null);\r
+ }\r
+\r
+ AlignViewport ds = new AlignViewport(al.getDataset());\r
+ ds.setDataset(true);\r
+ AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ tabbedPane.add("Dataset", dap);\r
+ viewports.add(ds);\r
+ alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
\r
viewport.addPropertyChangeListener(new PropertyChangeListener()\r
{\r
}\r
});\r
\r
+\r
if(Desktop.desktop!=null)\r
addServiceListeners();\r
}\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
- String line, text, token;\r
+ String line, type, desc, token;\r
UserColourScheme ucs;\r
int index, start, end;\r
StringTokenizer st;\r
- SequenceGroup sg;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
while ( (line = in.readLine()) != null)\r
{\r
+ lineNo++;\r
st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() != 6)\r
+ if (st.countTokens() != 7)\r
{\r
System.out.println("Groups file " + file +\r
- " is invalid. Read help file.");\r
- System.exit(1);\r
+ " is invalid. Read help file.\nLine: \n"\r
+ +lineNo +": "+line);\r
+ break;\r
}\r
\r
while (st.hasMoreElements())\r
{\r
- text = st.nextToken();\r
+ type = st.nextToken();\r
+ desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
start = seq.findIndex(start) - 1;\r
end = seq.findIndex(end) - 1;\r
\r
- sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
- sg.addSequence(seq, true);\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+ System.out.println(sf.getType()+" "+sf.getBegin());\r
+\r
+ // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ // sg.addSequence(seq, false);\r
+\r
+ // viewport.alignment.addGroup(sg);\r
\r
- viewport.alignment.addGroup(sg);\r
}\r
}\r
\r
+ viewport.showSequenceFeatures = true;\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+\r
+ alignPanel.repaint();\r
+\r
}\r
catch (Exception ex)\r
{\r
endRes);\r
}\r
\r
- c.setContents(new StringSelection(FastaFile.print(seqs)), null);\r
+ c.setContents(new StringSelection(new FastaFile().print(seqs)), null);\r
}\r
\r
/**\r
}\r
\r
String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ if(str.length()<1)\r
+ return;\r
\r
String format = IdentifyFile.Identify(str, "Paste");\r
SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);\r
\r
if (newAlignment)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ Alignment alignment = new Alignment(sequences);\r
+ alignment.setDataset( viewport.alignment.getDataset() );\r
+ AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
if (title.startsWith("Copied sequences"))\r
if(alignPanel.overviewPanel!=null)\r
alignPanel.overviewPanel.updateOverviewImage();\r
\r
+ Provenance prov = viewport.alignment.getProvenance();\r
+ if(prov == null)\r
+ {\r
+ prov = new Provenance();\r
+ viewport.alignment.setProvenance(prov);\r
+ }\r
+\r
+ prov.addEntry("Me",\r
+ "Edited in Jalview", new java.util.Date(), "myID");\r
+\r
alignPanel.repaint();\r
}\r
\r
new SequenceFeatureFetcher(viewport.\r
alignment,\r
alignPanel);\r
- ( (Alignment) viewport.alignment).featuresAdded = true;\r
}\r
\r
+ featureSettings.setEnabled(true);\r
+\r
alignPanel.repaint();\r
}\r
\r
// TODO: group services by location as well as function.\r
}\r
\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Export to Vamsas file");\r
+ chooser.setToolTipText("Export");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ vs.store(chooser.getSelectedFile().getAbsolutePath()\r
+ );\r
+ }\r
+ }\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+\r
+\r
+public void showTranslation_actionPerformed(ActionEvent e)\r
+{\r
+\r
+ if(!viewport.alignment.isNucleotide())\r
+ return;\r
+\r
+ viewport.showTranslation(showTranslation.isSelected());\r
+\r
+ if(!viewport.alignment.isNucleotide())\r
+ return;\r
+\r
+ int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] newSeq = new SequenceI[sSize];\r
+\r
+ int res, resSize;\r
+ StringBuffer protein;\r
+ SequenceI seq;\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ protein = new StringBuffer();\r
+ seq = (SequenceI)viewport.alignment.getSequenceAt(s);\r
+ resSize = seq.getLength();\r
+ for(res = 0; res < resSize; res+=3)\r
+ {\r
+ String codon = seq.getSequence(res, res+3);\r
+ codon = codon.replace('U', 'T');\r
+ String aa = ResidueProperties.codonTranslate(codon);\r
+ if(aa==null)\r
+ protein.append(viewport.getGapCharacter());\r
+ else if(aa.equals("STOP"))\r
+ protein.append("X");\r
+ else\r
+ protein.append( aa );\r
+ }\r
+ newSeq[s] = new Sequence(seq.getName(), protein.toString());\r
+ }\r
+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ // NEW_WINDOW_WIDTH,\r
+ // NEW_WINDOW_HEIGHT);\r
+\r
+ AlignViewport newViewport = new AlignViewport(al);\r
+ AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ tabbedPane.add("Protein", ap);\r
+ viewports.add(newViewport);\r
+ alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ AlignViewport ds = new AlignViewport(al.getDataset());\r
+ ds.setDataset(true);\r
+ AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ tabbedPane.add("Dataset", dap);\r
+ viewports.add(ds);\r
+ alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+public void tabSelected()\r
+{\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+}\r
+\r
}\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ boolean showTranslation = false;\r
+\r
+ boolean isDataset = false;\r
+\r
/**\r
* Creates a new AlignViewport object.\r
*\r
this.startSeq = 0;\r
this.endSeq = al.getHeight() - 1;\r
\r
- updateFromPreferences();\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateFromPreferences()\r
- {\r
showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
\r
// We must set conservation and consensus before setting colour,\r
// as Blosum and Clustal require this to be done\r
- updateConservation();\r
-\r
- updateConsensus();\r
+ if(vconsensus==null)\r
+ {\r
+ updateConservation();\r
+ updateConsensus();\r
+ }\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
{\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+\r
+ public void showTranslation(boolean b)\r
+ {\r
+ this.showTranslation = b;\r
+ }\r
+\r
+ public boolean getShowTranslation()\r
+ {\r
+ return showTranslation;\r
+ }\r
+\r
+ public void setDataset(boolean b)\r
+ {\r
+ isDataset = b;\r
+ }\r
+\r
+ public boolean isDataset()\r
+ {\r
+ return isDataset;\r
+ }\r
}\r
\r
setScrollValues(0, 0);\r
\r
+ annotationPanel.adjustPanelHeight();\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ setAnnotationVisible(av.getShowAnnotation());\r
+\r
+\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
textarea.setText(text);\r
}\r
\r
+ public void appendText(String text)\r
+ {\r
+ textarea.append(text);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{
}
- setTitle("Jalview 2005");
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
desktop = new JDesktopPane();
desktop.setBackground(Color.white);
}
}
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+ vs.load(
+ chooser.getSelectedFile().getAbsolutePath()
+ );
+ }
+
+ }
+
+
}
SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
+ float transparency = 1.0f;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed;\r
\r
/**\r
* Creates a new FeatureRenderer object.\r
public FeatureRenderer(AlignViewport av)\r
{\r
this.av = av;\r
+ initColours();\r
}\r
\r
/**\r
* @param width DOCUMENT ME!\r
* @param height DOCUMENT ME!\r
*/\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ public void drawSequence(Graphics g1, SequenceI seq, SequenceGroup[] sg,\r
int start, int end, int x1, int y1, int width, int height)\r
{\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
+\r
+ if(seq.getSequenceFeatures()==null)\r
+ return;\r
+\r
+ Enumeration e = null, e2;\r
+ String type;\r
+ if(featuresDisplayed!=null)\r
+ e = featuresDisplayed.elements();\r
+ else\r
+ e = seq.getSequenceFeatures().elements();\r
+\r
+ Graphics2D g = (Graphics2D)g1;\r
+ g.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER,transparency));\r
\r
while (e.hasMoreElements())\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ SequenceFeature sf=null;\r
+ if(featuresDisplayed!=null)\r
+ {\r
+ e2 = seq.getSequenceFeatures().elements();\r
+ type = e.nextElement().toString();\r
+ while(e2.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if(sf.getType().equals(type))\r
+ break;\r
+ else\r
+ sf = null;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sf = (SequenceFeature) e.nextElement();\r
+ type = sf.getType();\r
+ }\r
+\r
+ if(sf==null)\r
+ continue;\r
\r
- if (sf.getStart() > seq.getEnd())\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
{\r
continue;\r
}\r
\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fstart = seq.findIndex(sf.getBegin()) - 1;\r
int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
if (((fstart <= end) && (fend >= start)))\r
\r
if (fstart == fend)\r
{\r
- g.setColor(Color.red);\r
+ g.setColor(getColour(type));\r
g.fillRoundRect((fstart - start) * width, y1, width,\r
height, 4, 4);\r
g.setColor(Color.white);\r
continue;\r
}\r
\r
- g.setColor(Color.blue);\r
+ g.setColor(getColour(type));\r
g.fillRect((i - start) * width, y1, width, height);\r
\r
g.setColor(Color.white);\r
}\r
}\r
}\r
+ g.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER,1.0f));\r
+\r
}\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\r
+ }\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setTransparency(float value)\r
+ {\r
+ transparency = value;\r
+ }\r
+\r
+ public float getTransparency()\r
+ {\r
+ return transparency;\r
+ }\r
+\r
+ public void setFeaturePriority(Object [][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ featuresDisplayed = new Vector();\r
+ for(int i=data.length-1; i>-1; i--)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color)data[i][1]);\r
+ if( ((Boolean)data[i][2]).booleanValue() )\r
+ featuresDisplayed.addElement(type);\r
+ }\r
+ }\r
+\r
+ Hashtable featureColours = new Hashtable();\r
+ void initColours()\r
+ {\r
+ featureColours.put("active site", new Color(255, 75, 0));\r
+ featureColours.put("binding site", new Color(245, 85, 0));\r
+ featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
+ featureColours.put("chain", new Color(225, 105, 0));\r
+ featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
+ featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
+ featureColours.put("cross-link", new Color(195, 135, 0));\r
+ featureColours.put("disulfide bond", new Color(185, 145, 0));\r
+ featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
+ featureColours.put("domain", new Color(165, 165, 0));\r
+ featureColours.put("glycosylation site", new Color(155, 175, 0));\r
+ featureColours.put("helix", new Color(145, 185, 0));\r
+ featureColours.put("initiator methionine", new Color(135, 195, 5));\r
+ featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
+ featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
+ featureColours.put("modified residue", new Color(105, 225, 35));\r
+ featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
+ featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
+ featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
+ featureColours.put("nucleotide phosphate-binding region",\r
+ new Color(65, 245, 75));\r
+ featureColours.put("peptide", new Color(55, 235, 85));\r
+ featureColours.put("propeptide", new Color(45, 225, 95));\r
+ featureColours.put("region of interest", new Color(35, 215, 105));\r
+ featureColours.put("repeat", new Color(25, 205, 115));\r
+ featureColours.put("selenocysteine", new Color(15, 195, 125));\r
+ featureColours.put("sequence conflict", new Color(5, 185, 135));\r
+ featureColours.put("sequence variant", new Color(0, 175, 145));\r
+ featureColours.put("short sequence motif", new Color(0, 165, 155));\r
+ featureColours.put("signal peptide", new Color(0, 155, 165));\r
+ featureColours.put("site", new Color(0, 145, 175));\r
+ featureColours.put("splice variant", new Color(0, 135, 185));\r
+ featureColours.put("strand", new Color(0, 125, 195));\r
+ featureColours.put("topological domain", new Color(0, 115, 205));\r
+ featureColours.put("transit peptide", new Color(0, 105, 215));\r
+ featureColours.put("transmembrane region", new Color(0, 95, 225));\r
+ featureColours.put("turn", new Color(0, 85, 235));\r
+ featureColours.put("unsure residue", new Color(0, 75, 245));\r
+ featureColours.put("zinc finger region", new Color(0, 65, 255));\r
+ }\r
+\r
}\r
--- /dev/null
+package jalview.gui;\r
+\r
+import jalview.datamodel.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+import java.awt.*;\r
+import java.util.*;\r
+import javax.swing.BorderFactory;\r
+import java.awt.event.*;\r
+import javax.swing.table.*;\r
+\r
+public class FeatureSettings extends JPanel\r
+{\r
+ Vector allFeatures;\r
+ final FeatureRenderer fr;\r
+ final AlignmentPanel ap;\r
+ Object [][] originalData;\r
+\r
+ public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
+ av.alignment.getSequences();\r
+ final JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "Sequence Feature Settings", 500, 300);\r
+\r
+\r
+ allFeatures = new Vector();\r
+ Vector features;\r
+ Enumeration e;\r
+ SequenceFeature sf;\r
+ for(int i=0; i< av.alignment.getHeight(); i++)\r
+ {\r
+ features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+ if(features==null)\r
+ continue;\r
+\r
+ e = features.elements();\r
+ while(e.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature)e.nextElement();\r
+ if(!allFeatures.contains(sf.getType()))\r
+ {\r
+ allFeatures.addElement(sf.getType());\r
+ }\r
+ }\r
+ }\r
+ if(allFeatures.size()<1)\r
+ {\r
+ try{\r
+ frame.setClosed(true);\r
+ }catch(Exception ex){}\r
+ return;\r
+ }\r
+\r
+ int fSize = allFeatures.size();\r
+\r
+ String type;\r
+ Object [][] data = new Object[fSize][3];\r
+ originalData = new Object[fSize][3];\r
+ for(int i=0; i<fSize; i++)\r
+ {\r
+ type = allFeatures.elementAt(i).toString();\r
+ Color col = fr.getColour(type);\r
+ data[i][0]=type;\r
+ data[i][1]=col;\r
+ data[i][2]= new Boolean(true);\r
+ originalData[i][0]=type;\r
+ originalData[i][1]=col;\r
+ originalData[i][2]= new Boolean(true);\r
+ }\r
+\r
+ final JSlider transparency = new JSlider(0,70,0);\r
+ transparency.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ fr.setTransparency( (float)(100-transparency.getValue())/100f);\r
+ ap.repaint();\r
+ }\r
+ });\r
+\r
+ JPanel transPanel = new JPanel(new FlowLayout());\r
+ transPanel.add(new JLabel("Transparency"));\r
+ transPanel.add(transparency);\r
+\r
+\r
+\r
+ ////////////////////////////////////\r
+ //Now build the table\r
+ final JTable table = new JTable(new FeatureTableModel(data));\r
+ JScrollPane scrollPane = new JScrollPane(table);\r
+ table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setDefaultRenderer(Color.class,\r
+ new ColorRenderer());\r
+\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\r
+\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
+ });\r
+\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if(newRow!=selectedRow\r
+ && selectedRow!=-1\r
+ && newRow!=-1)\r
+ {\r
+ Object[] temp = new Object[3];\r
+ temp[0] = table.getValueAt(selectedRow, 0);\r
+ temp[1] = table.getValueAt(selectedRow, 1);\r
+ temp[2] = table.getValueAt(selectedRow, 2);\r
+\r
+ table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
+ table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
+ table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
+\r
+ table.setValueAt(temp[0], newRow, 0);\r
+ table.setValueAt(temp[1], newRow, 1);\r
+ table.setValueAt(temp[2], newRow, 2);\r
+\r
+ selectedRow = newRow;\r
+ }\r
+ }\r
+ });\r
+\r
+ //////////////////////////////////////////////\r
+ //We're going to need those OK cancel buttons\r
+ JPanel buttonPanel = new JPanel(new FlowLayout());\r
+ JButton button = new JButton("OK");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ try {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception exe)\r
+ {}\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+ button = new JButton("Cancel");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ try{\r
+ updateFeatureRenderer(originalData);\r
+ frame.setClosed(true);\r
+ }catch(Exception exe){}\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+\r
+\r
+ this.setLayout(new BorderLayout());\r
+ JPanel bigPanel = new JPanel(new BorderLayout());\r
+ bigPanel.add(transPanel, BorderLayout.SOUTH);\r
+ bigPanel.add(scrollPane, BorderLayout.CENTER);\r
+\r
+ add(bigPanel, BorderLayout.CENTER);\r
+ add(buttonPanel, BorderLayout.SOUTH);\r
+\r
+ }\r
+\r
+ public void updateFeatureRenderer(Object [][] data)\r
+ {\r
+ fr.setFeaturePriority( data );\r
+ ap.repaint();\r
+ }\r
+\r
+ int selectedRow =-1;\r
+\r
+\r
+ /////////////////////////////////////////////////////////////////////////\r
+ // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
+ /////////////////////////////////////////////////////////////////////////\r
+ class FeatureTableModel\r
+ extends AbstractTableModel\r
+ {\r
+ FeatureTableModel(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
+\r
+ private String[] columnNames = {"Feature Type", "Colour","Display"};\r
+ private Object[][] data;\r
+\r
+ public Object[][] getData()\r
+ {\r
+ return data;\r
+ }\r
+\r
+ public int getColumnCount() {\r
+ return columnNames.length;\r
+ }\r
+\r
+ public Object[] getRow(int row)\r
+ {\r
+ return data[row];\r
+ }\r
+\r
+ public int getRowCount() {\r
+ return data.length;\r
+ }\r
+\r
+ public String getColumnName(int col) {\r
+ return columnNames[col];\r
+ }\r
+\r
+ public Object getValueAt(int row, int col) {\r
+ return data[row][col];\r
+ }\r
+\r
+ public Class getColumnClass(int c) {\r
+ return getValueAt(0, c).getClass();\r
+ }\r
+\r
+ public boolean isCellEditable(int row, int col) {\r
+ return col==0 ? false:true;\r
+ }\r
+\r
+ public void setValueAt(Object value, int row, int col) {\r
+ data[row][col] = value;\r
+ fireTableCellUpdated(row, col);\r
+ updateFeatureRenderer(data);\r
+ }\r
+\r
+ }\r
+ class ColorRenderer extends JLabel\r
+ implements TableCellRenderer {\r
+ javax.swing.border.Border unselectedBorder = null;\r
+ javax.swing.border.Border selectedBorder = null;\r
+\r
+ public ColorRenderer() {\r
+ setOpaque(true); //MUST do this for background to show up.\r
+ }\r
+\r
+ public Component getTableCellRendererComponent(\r
+ JTable table, Object color,\r
+ boolean isSelected, boolean hasFocus,\r
+ int row, int column) {\r
+ Color newColor = (Color)color;\r
+ setBackground(newColor);\r
+ if (isSelected) {\r
+ if (selectedBorder == null) {\r
+ selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
+ table.getSelectionBackground());\r
+ }\r
+ setBorder(selectedBorder);\r
+ } else {\r
+ if (unselectedBorder == null) {\r
+ unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
+ table.getBackground());\r
+ }\r
+ setBorder(unselectedBorder);\r
+ }\r
+\r
+ setToolTipText("RGB value: " + newColor.getRed() + ", "\r
+ + newColor.getGreen() + ", "\r
+ + newColor.getBlue());\r
+ return this;\r
+ }\r
+ }\r
+}\r
+\r
+ class ColorEditor extends AbstractCellEditor\r
+ implements TableCellEditor,\r
+ ActionListener {\r
+ Color currentColor;\r
+ JButton button;\r
+ JColorChooser colorChooser;\r
+ JDialog dialog;\r
+ protected static final String EDIT = "edit";\r
+\r
+ public ColorEditor() {\r
+ //Set up the editor (from the table's point of view),\r
+ //which is a button.\r
+ //This button brings up the color chooser dialog,\r
+ //which is the editor from the user's point of view.\r
+ button = new JButton();\r
+ button.setActionCommand(EDIT);\r
+ button.addActionListener(this);\r
+ button.setBorderPainted(false);\r
+ //Set up the dialog that the button brings up.\r
+ colorChooser = new JColorChooser();\r
+ dialog = JColorChooser.createDialog(button,\r
+ "Select new Colour",\r
+ true, //modal\r
+ colorChooser,\r
+ this, //OK button handler\r
+ null); //no CANCEL button handler\r
+ }\r
+\r
+ /**\r
+ * Handles events from the editor button and from\r
+ * the dialog's OK button.\r
+ */\r
+ public void actionPerformed(ActionEvent e) {\r
+\r
+ if (EDIT.equals(e.getActionCommand())) {\r
+ //The user has clicked the cell, so\r
+ //bring up the dialog.\r
+ button.setBackground(currentColor);\r
+ colorChooser.setColor(currentColor);\r
+ dialog.setVisible(true);\r
+\r
+ //Make the renderer reappear.\r
+ fireEditingStopped();\r
+\r
+ } else { //User pressed dialog's "OK" button.\r
+ currentColor = colorChooser.getColor();\r
+ }\r
+ }\r
+\r
+ //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
+ public Object getCellEditorValue() {\r
+ return currentColor;\r
+ }\r
+\r
+ //Implement the one method defined by TableCellEditor.\r
+ public Component getTableCellEditorComponent(JTable table,\r
+ Object value,\r
+ boolean isSelected,\r
+ int row,\r
+ int column) {\r
+ currentColor = (Color)value;\r
+ return button;\r
+ }\r
+}\r
fontName.addItem(fonts[i]);\r
}\r
\r
- for (int i = 1; i < 31; i++)\r
+ for (int i = 1; i < 51; i++)\r
{\r
fontSize.addItem(i + "");\r
}\r
--- /dev/null
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+\r
+public class GFeatureSelector\r
+ extends JPanel\r
+{\r
+ public GFeatureSelector()\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ jLabel1.setText("Feature");\r
+ this.add(jLabel1);\r
+ }\r
+\r
+ JLabel jLabel1 = new JLabel();\r
+}\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
\r
- if(av.vconsensus==null)\r
+ if(av.conservation==null)\r
graphHeight = 0;\r
\r
\r
epsRendering.addItem("Text");\r
epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
\r
+ blcdb.setSelected( Cache.getDefault("BLC_DBPREFIX", false) );\r
+ blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
+ clustaldb.setSelected( Cache.getDefault("CLUSTAL_DBPREFIX", false) );\r
+ clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
+ fastadb.setSelected( Cache.getDefault("FASTA_DBPREFIX", false) );\r
+ fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
+ msfdb.setSelected( Cache.getDefault("MSF_DBPREFIX", false) );\r
+ msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
+ pfamdb.setSelected( Cache.getDefault("PFAM_DBPREFIX", false) );\r
+ pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
+ pileupdb.setSelected( Cache.getDefault("PILEUP_DBPREFIX", false) );\r
+ pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
+ pirdb.setSelected( Cache.getDefault("PIR_DBPREFIX", false) );\r
+ pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
+\r
/****************************************************\r
* Set up Connections\r
*/\r
}\r
\r
\r
+ Cache.applicationProperties.setProperty("BLC_DBPREFIX", Boolean.toString(blcdb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("CLUSTAL_DBPREFIX", Boolean.toString(clustaldb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("FASTA_DBPREFIX", Boolean.toString(fastadb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("MSF_DBPREFIX", Boolean.toString(msfdb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PFAM_DBPREFIX", Boolean.toString(pfamdb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PILEUP_DBPREFIX", Boolean.toString(pileupdb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_DBPREFIX", Boolean.toString(pirdb.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+\r
\r
Cache.saveProperties();\r
try\r
import java.awt.image.*;\r
\r
import javax.swing.*;\r
+import jalview.schemes.*;\r
\r
\r
/**\r
setBackground(Color.white);\r
}\r
\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
int y2, int startx, int starty, int offset)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
- g.setFont(av.getFont());\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
\r
+ SequenceI nextSeq, dna = null;\r
+ int aaHeight = av.charHeight, dnaHeight = av.charHeight;\r
+ Font dnafont = null, aafont = av.getFont();\r
\r
- SequenceI nextSeq;\r
+ /* if (av.getShowTranslation())\r
+ {\r
+ aaHeight = (int) (av.getCharHeight() * aaRatio);\r
+ dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
+ java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1f / 3f, 1);\r
+ dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ dnaHeight);\r
+ dnafont = dnafont.deriveFont(transform);\r
+\r
+ aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ aaHeight);\r
+ transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1 / aaRatio, 1);\r
+ aafont = aafont.deriveFont(transform);\r
+ }\r
+*/\r
\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
/// First draw the sequences\r
/////////////////////////////\r
for (int i = y1; i < y2; i++)\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
- g.setFont(av.getFont());\r
-\r
+ g.setFont(aafont);\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ dna = nextSeq;\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int r = 0; r<nextSeq.getLength(); r+=3)\r
+ {\r
+ String codon = nextSeq.getSequence(r, r+3);\r
+ codon = codon.replace('U', 'T');\r
+ String res = ResidueProperties.codonTranslate(codon);\r
+ if(res !=null )\r
+ {\r
+ if (res.equals("STOP"))\r
+ sb.append("X");\r
+ else\r
+ sb.append(res);\r
+ }\r
+ }\r
+ nextSeq = new Sequence("d", sb.toString());\r
+ }*/\r
\r
sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
x1, x2, (x1 - startx) * av.charWidth,\r
offset + ( (i - starty) * av.charHeight), av.charWidth,\r
- av.charHeight);\r
-\r
+ aaHeight);\r
\r
\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ av.setGlobalColourScheme(new NucleotideColourScheme());\r
+ g.setFont(dnafont);\r
+ sr.drawSequence(g, dna, null,\r
+ x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
+ offset + ( (i - starty) * av.charHeight) + aaHeight,\r
+ av.charWidth / 3,\r
+ dnaHeight);\r
+ av.setGlobalColourScheme(cs);\r
+ }*/\r
\r
if (av.showSequenceFeatures)\r
{\r
// Now outline any areas if necessary\r
/////////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
int sx = -1;\r
int sy = -1;\r
int ex = -1;\r
int groupIndex = -1;\r
\r
- if ((group == null) && (groups.size() > 0))\r
+ if ((group == null) && (av.alignment.getGroups().size() > 0))\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
groupIndex = 0;\r
}\r
\r
-\r
if (group != null && !isOverview)\r
{\r
do\r
\r
groupIndex++;\r
\r
- if (groupIndex >= groups.size())\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
{\r
break;\r
}\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
}\r
- while (groupIndex < groups.size());\r
+ while (groupIndex < av.alignment.getGroups().size());\r
}\r
\r
/// Highlight search Results once all sequences have been drawn\r
\r
ap = p;\r
\r
+\r
addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
if (editingSeqs)\r
{\r
+ if(!av.isDataset())\r
doMouseDragged(evt);\r
}\r
else\r
{\r
+ if(!av.isDataset())\r
doMouseDraggedDefineMode(evt);\r
}\r
}\r
{\r
Font font = av.getFont();\r
int fontSize = font.getSize();\r
- if (e.getWheelRotation() > 0 && fontSize < 30)\r
+ if (e.getWheelRotation() > 0 && fontSize < 51)\r
fontSize++;\r
else if (fontSize > 1)\r
fontSize--;\r
});\r
\r
\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- mouseWheelPressed = false;\r
-\r
- if (editingSeqs)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- else\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- }\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
- {\r
- mouseWheelPressed = true;\r
- return;\r
- }\r
+ if(!av.isDataset())\r
+ {\r
+ addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ mouseWheelPressed = false;\r
\r
- if (evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
+ if (editingSeqs)\r
+ {\r
+ doMouseReleased(evt);\r
+ }\r
+ else\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ }\r
+ }\r
\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- }\r
- }\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
+ {\r
+ mouseWheelPressed = true;\r
+ return;\r
+ }\r
+\r
+ if (evt.isShiftDown() || evt.isAltDown() ||\r
+ evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ groupEditing = true;\r
+ }\r
+\r
+ editingSeqs = true;\r
+ doMousePressed(evt);\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ }\r
+ }\r
\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (editingSeqs)\r
- {\r
- return;\r
- }\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
\r
- doMouseExitedDefineMode(evt);\r
- }\r
+ doMouseExitedDefineMode(evt);\r
+ }\r
\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (editingSeqs)\r
- {\r
- return;\r
- }\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
\r
- doMouseEnteredDefineMode(evt);\r
- }\r
- });\r
+ doMouseEnteredDefineMode(evt);\r
+ }\r
+ });\r
+ }\r
}\r
\r
int startWrapBlock=-1;\r
if (av.showSequenceFeatures)\r
{\r
Vector features = sequence.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- while (e.hasMoreElements())\r
+ if(features!=null)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ StringBuffer sbuffer = new StringBuffer("<html>");\r
\r
- if ((sf.getStart() <= sequence.findPosition(res)) &&\r
- (sf.getEnd() >= sequence.findPosition(res)))\r
+ for (int i = 0; i < features.size(); i++)\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) features.elementAt(i);\r
+\r
+ if ( (sf.getBegin() <= sequence.findPosition(res)) &&\r
+ (sf.getEnd() >= sequence.findPosition(res)))\r
{\r
- if (sbuffer.length() > 0)\r
- {\r
- sbuffer.append("; ");\r
- }\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
+ sbuffer.append(sf.getType());\r
+ if (sf.getDescription() != null)\r
+ sbuffer.append(" " + sf.getDescription());\r
\r
- if (sf.getStatus().length() > 0)\r
- {\r
- sbuffer.append(" (" + sf.getStatus() + ")");\r
- }\r
+ if (sf.getStatus() != null)\r
+ {\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
+ }\r
}\r
- }\r
\r
- this.setToolTipText(sbuffer.toString());\r
+ }\r
+\r
+ sbuffer.append("</html>");\r
+ if(sbuffer.equals("<html></html>"))\r
+ setToolTipText("");\r
+ else\r
+ setToolTipText(sbuffer.toString());\r
+ }\r
}\r
}\r
\r
\r
graphics = g;\r
\r
- drawBoxes(seq, start, end, x1, y1, width, height);\r
+ drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
\r
fm = g.getFontMetrics();\r
- drawText(seq, start, end, x1, y1, width, height);\r
+ drawText(seq, start, end, x1, y1, (int) width, height);\r
}\r
\r
/**\r
{\r
if (tempColour != null)\r
{\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
+ int xxx = x1 + (int) (av.charWidth * (curStart - start));\r
+ if (width != av.charWidth)\r
+ {\r
+ xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3;\r
+ }\r
+\r
+\r
+ graphics.fillRect(xxx, y1,\r
curWidth, height);\r
}\r
\r
i++;\r
}\r
\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
+ int xxx = x1 + (int) (av.charWidth * (curStart - start));\r
+ if (width != av.charWidth)\r
+ {\r
+ xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3;\r
+ }\r
+\r
+\r
+ graphics.fillRect(xxx, y1, curWidth,\r
height);\r
}\r
\r
int charOffset = 0;\r
char s;\r
\r
+\r
// Need to find the sequence position here.\r
String sequence = seq.getSequence();\r
\r
}\r
\r
charOffset = (width - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);\r
+\r
+ int xxx = charOffset + x1 + (int)(av.charWidth * (i - start));\r
+ if(width != av.charWidth)\r
+ {\r
+ xxx = charOffset + x1 + (int)(av.charWidth * (i - start))/3;\r
+ }\r
+\r
+ graphics.drawString(String.valueOf(s),xxx, (y1 + height) - pady);\r
}\r
}\r
\r
\r
int y = yoffset;\r
\r
- g.drawString("Jalview 2005 ", 50, y);\r
+ g.drawString("Jalview "+jalview.bin.Cache.getProperty("VERSION"), 50, y);\r
g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));\r
- g.drawString("Version " + jalview.bin.Cache.getProperty("VERSION") +\r
- "; Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),\r
+ g.drawString("Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),\r
180, y);\r
\r
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals("Checking"))\r
Vector headers;\r
long start;\r
long end;\r
+ boolean dbPrefix = false;\r
+ boolean jvSuffix = true;\r
\r
/**\r
* Creates a new AlignFile object.\r
* Print out in alignment file format the Sequences in the seqs Vector.\r
*/\r
public abstract String print();\r
+\r
+ public void addDBPrefix(boolean b)\r
+ {\r
+ dbPrefix = b;\r
+ }\r
+\r
+ public void addJVSuffix(boolean b)\r
+ {\r
+ jvSuffix = b;\r
+ }\r
+\r
+ /**\r
+ * A general parser for ids. Will look for dbrefs in\r
+ * Uniprot format source|id\r
+ * And also Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ Sequence parseId(String id)\r
+ {\r
+ Sequence seq = new Sequence("","");\r
+ int space = id.indexOf(" ");\r
+ if(space>-1)\r
+ {\r
+ seq.setDescription(id.substring(space+1));\r
+ id = id.substring(0, space);\r
+ }\r
+\r
+ // Read in any DB refs first\r
+ StringTokenizer st;\r
+ st = new StringTokenizer(id, "|");\r
+\r
+ while (st.countTokens()>2)\r
+ {\r
+ seq.addDBRef( new DBRefEntry( st.nextToken(), "0", st.nextToken()));\r
+ }\r
+\r
+ if(st.hasMoreTokens())\r
+ id = st.nextToken();\r
+\r
+\r
+ // Remove /start-end from sequence\r
+ if (id.indexOf("/") > 0)\r
+ {\r
+ st = new StringTokenizer(id, "/");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ id = st.nextToken();\r
+\r
+ String tmp = st.nextToken();\r
+\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ seq.setStart( Integer.valueOf(st.nextToken()).intValue() );\r
+ seq.setEnd( Integer.valueOf(st.nextToken()).intValue() );\r
+ }\r
+ }\r
+ }\r
+ seq.setName(id);\r
+ return seq;\r
+ }\r
+\r
+ /**\r
+ * Creates the output id.\r
+ * Adds prefix Uniprot format source|id\r
+ * And suffix Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ String printId(SequenceI seq)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ if(dbPrefix && seq.getDBRef()!=null)\r
+ {\r
+ Vector dbrefs = seq.getDBRef();\r
+ for(int i=0; i<dbrefs.size(); i++)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry)dbrefs.elementAt(i);\r
+ result.append(entry.getSource()+"|"+entry.getAccessionId()+"|");\r
+ }\r
+ }\r
+\r
+ result.append(seq.getName());\r
+\r
+ if(jvSuffix)\r
+ {\r
+ result.append("/"+seq.getStart()+"-"+seq.getEnd());\r
+ }\r
+\r
+ return result.toString();\r
+ }\r
+\r
}\r
--- /dev/null
+ /*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ */\r
+ package jalview.io;\r
+\r
+ import jalview.datamodel.*;\r
+\r
+ import java.util.Vector;\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ public class AppletFormatAdapter\r
+ {\r
+ /** DOCUMENT ME!! */\r
+ public static final Vector formats = new Vector();\r
+\r
+ static\r
+ {\r
+ formats.addElement("BLC");\r
+ formats.addElement("CLUSTAL");\r
+ formats.addElement("FASTA");\r
+ formats.addElement("MSF");\r
+ formats.addElement("PileUp");\r
+ formats.addElement("PIR");\r
+ formats.addElement("PFAM");\r
+ }\r
+\r
+ AlignFile afile = null;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceI[] readFile(String inFile, String type, String format)\r
+ {\r
+ try\r
+ {\r
+ if (format.equals("FASTA"))\r
+ {\r
+ afile = new FastaFile(inFile, type);\r
+ }\r
+ else if (format.equals("MSF"))\r
+ {\r
+ afile = new MSFfile(inFile, type);\r
+ }\r
+ else if (format.equals("PileUp"))\r
+ {\r
+ afile = new PileUpfile(inFile, type);\r
+ }\r
+ else if (format.equals("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile(inFile, type);\r
+ }\r
+ else if (format.equals("BLC"))\r
+ {\r
+ afile = new BLCFile(inFile, type);\r
+ }\r
+ else if (format.equals("PIR"))\r
+ {\r
+ afile = new PIRFile(inFile, type);\r
+ }\r
+ else if (format.equals("PFAM"))\r
+ {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+\r
+ return afile.getSeqsAsArray();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Failed to read alignment using the '" + format +\r
+ "' reader.");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param format DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String formatSequences(String format, Vector seqs)\r
+ {\r
+ SequenceI[] s = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ s[i] = (SequenceI) seqs.elementAt(i);\r
+\r
+ try\r
+ {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equalsIgnoreCase("FASTA"))\r
+ {\r
+ afile = new FastaFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("MSF"))\r
+ {\r
+ afile = new MSFfile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PileUp"))\r
+ {\r
+ afile = new PileUpfile();\r
+ }\r
+ else if (format.equalsIgnoreCase("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("BLC"))\r
+ {\r
+ afile = new BLCFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PIR"))\r
+ {\r
+ afile = new PIRFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PFAM"))\r
+ {\r
+ afile = new PfamFile();\r
+ }\r
+\r
+ afile.setSeqs(s);\r
+\r
+ return afile.print();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Failed to write alignment as a '" + format +\r
+ "' file\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
+ }\r
\r
if (abracket > -1)\r
{\r
- if (line.indexOf(" ") > -1) //\r
- {\r
- ///Colur it be this format?\r
- //>54402046 0 1 137 137:\r
- // or this??\r
- // 1 >L1H14 30539 343\r
- try\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\r
- // remove p Value\r
- line = line.substring(abracket + 1);\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
-\r
- int value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- starts.addElement(value + "");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- ends.addElement(value + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("Error during blockfile read.");\r
- ex.printStackTrace();\r
- starts.addElement("1");\r
- ends.addElement("-1");\r
- }\r
- }\r
- else\r
- {\r
- if (line.indexOf("/") > -1)\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0,\r
- line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") +\r
- 1));\r
- }\r
- else\r
- {\r
- ids.addElement(line.substring(abracket + 1));\r
- starts.addElement("1");\r
- ends.addElement("-1");\r
- }\r
- }\r
+ if (line.indexOf(" ") > -1) //\r
+ {\r
+ line = line.substring(abracket + 1,\r
+ line.indexOf(" ", abracket + 1));\r
+ }\r
+ else\r
+ line = line.substring(abracket+1);\r
+\r
+ Sequence seq = parseId(line);\r
+ ids.addElement(seq.getName());\r
+ starts.addElement(seq.getStart() + "");\r
+ ends.addElement(seq.getEnd() + "");\r
}\r
}\r
while (!idsFound);\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer();\r
-\r
+ /**\r
+ * A general parser for ids. Will look for dbrefs in\r
+ * Uniprot format source|id\r
+ * And also Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
int i = 0;\r
int max = -1;\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
+ out.append(">" + printId(s[i]) +"\n");\r
\r
if (s[i].getSequence().length() > max)\r
{\r
public class ClustalFile\r
extends AlignFile\r
{\r
- Vector ids;\r
\r
public ClustalFile()\r
{\r
public void initData()\r
{\r
super.initData();\r
- ids = new Vector();\r
}\r
\r
public void parse()\r
//Add sequences to the hash\r
for (i = 0; i < headers.size(); i++)\r
{\r
- int start = 1;\r
- int end = -1;\r
-\r
if (seqhash.get(headers.elementAt(i)) != null)\r
{\r
if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
.length();\r
}\r
\r
- String head = headers.elementAt(i).toString();\r
-\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken())\r
- .intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).\r
- toString())\r
- .toString(), start, end);\r
+ Sequence newSeq = parseId(headers.elementAt(i).toString());\r
+ newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
\r
seqs.addElement(newSeq);\r
}\r
return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
+ String tmp = printId(s[i]);\r
\r
if (s[i].getSequence().length() > max)\r
{\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
- "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));\r
\r
int start = i * len;\r
int end = start + len;\r
*/\r
package jalview.io;\r
\r
+import java.io.*;\r
+\r
import org.apache.axis.AxisFault;\r
import org.apache.axis.client.*;\r
import org.apache.axis.encoding.XMLType;\r
}\r
}\r
\r
+ public static void main (String [] args)\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData("uniprot:25K89D_SARPE;G6PblobD_HUMAN",\r
+ "xml", null);\r
+\r
+ try{\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter("out.xml"));\r
+\r
+\r
+ for(int i=0; i<result.length; i++)\r
+ {\r
+ out.println(result[i]);\r
+ }\r
+ out.close();\r
+ }catch(Exception ex){ex.printStackTrace();}\r
+\r
+ }\r
+\r
+\r
+ public File fetchDataAsFile(String ids, String f, String s)\r
+ {\r
+ String [] data = fetchData(ids, f, s);\r
+ File outFile = null;\r
+ try{\r
+ outFile = File.createTempFile("jalview", ".xml");\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ int index=0;\r
+ while( index < data.length )\r
+ {\r
+ out.println(data[index]);\r
+ index++;\r
+ }\r
+ out.close();\r
+ }catch(Exception ex){}\r
+ return outFile;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
import java.io.*;\r
\r
-import java.util.*;\r
-\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public void parse() throws IOException\r
{\r
- String id = "";\r
- StringBuffer seq = new StringBuffer();\r
+ StringBuffer sb = new StringBuffer();\r
int count = 0;\r
\r
- int sstart = 0;\r
- int send = 0;\r
-\r
String line;\r
+ Sequence seq = null;\r
\r
while ((line = nextLine()) != null)\r
{\r
// Do we have an id line?\r
// JBPNote - this code needs to be standardised to EBI/whatever for the\r
// >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)\r
- if (line.substring(0, 1).equals(">"))\r
+ if (line.charAt(0)=='>')\r
{\r
+ seq = parseId(line.substring(1));\r
+\r
if (count != 0)\r
{\r
- if (sstart != 0)\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(),\r
- sstart, send));\r
- }\r
- else\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(), 1,\r
- seq.length()));\r
- }\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
}\r
\r
count++;\r
-\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
-\r
- id = str.nextToken();\r
- id = id.substring(1);\r
-\r
- com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
- "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
-\r
- // JBPNote At the moment - we don't get rid of the friendly names but this\r
- // behaviour is probably wrong in the long run.\r
- if (dbId.search(id))\r
- {\r
- String dbid = dbId.stringMatched(1);\r
- String idname = dbId.stringMatched(2);\r
-\r
- if ((idname.length() > 0) &&\r
- (idname.indexOf("_") > -1))\r
- {\r
- id = idname; // use the friendly name - apparently no dbid\r
- }\r
- else if (dbid.length() > 1)\r
- {\r
- id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise\r
- }\r
- }\r
-\r
- if (id.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(id, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- id = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
-\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- sstart = Integer.valueOf(st.nextToken())\r
- .intValue();\r
- send = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- seq = new StringBuffer();\r
+ sb = new StringBuffer();\r
}\r
else\r
{\r
- seq = seq.append(line);\r
+ sb.append(line);\r
}\r
}\r
}\r
\r
if (count > 0)\r
{\r
- if (!isValidProteinSequence(seq.toString().toUpperCase()))\r
+ if (!isValidProteinSequence(sb.toString().toUpperCase()))\r
{\r
throw new IOException("Invalid protein sequence");\r
}\r
\r
- if (sstart != 0)\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
- sstart, send));\r
- }\r
- else\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
- 1, seq.length()));\r
- }\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
}\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, 72);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s, int len)\r
- {\r
- return print(s, len, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s, int len, boolean gaps)\r
- {\r
- return print(s, len, gaps, true);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s, int len, boolean gaps,\r
- boolean displayId)\r
+ public String print(SequenceI[] s)\r
{\r
+ int len = 72;\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- String seq = "";\r
-\r
- if (gaps)\r
- {\r
- seq = s[i].getSequence();\r
- }\r
- else\r
- {\r
- seq = AlignSeq.extractGaps("-. ", s[i].getSequence());\r
- }\r
+ out.append(">" + printId(s[i]));\r
+ if(s[i].getDescription()!=null)\r
+ out.append(" "+s[i].getDescription());\r
\r
- // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
- out.append(">" +\r
- ((displayId) ? s[i].getDisplayId() : s[i].getName()) + "\n");\r
+ out.append("\n");\r
\r
- int nochunks = (seq.length() / len) + 1;\r
+ int nochunks = (s[i].getLength() / len) + 1;\r
\r
for (int j = 0; j < nochunks; j++)\r
{\r
int start = j * len;\r
int end = start + len;\r
\r
- if (end < seq.length())\r
+ if (end < s[i].getLength())\r
{\r
- out.append(seq.substring(start, end) + "\n");\r
+ out.append(s[i].getSequence(start, end) + "\n");\r
}\r
- else if (start < seq.length())\r
+ else if (start < s[i].getLength())\r
{\r
- out.append(seq.substring(start) + "\n");\r
+ out.append(s[i].getSequence(start, s[i].getLength()) + "\n");\r
}\r
}\r
\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FormatAdapter\r
+public class FormatAdapter extends AppletFormatAdapter\r
{\r
- /** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
-\r
- static\r
- {\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- AlignFile afile = null;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI[] readFile(String inFile, String type, String format)\r
- {\r
- try\r
- {\r
- if (format.equals("FASTA"))\r
- {\r
- afile = new FastaFile(inFile, type);\r
- }\r
- else if (format.equals("MSF"))\r
- {\r
- afile = new MSFfile(inFile, type);\r
- }\r
- else if (format.equals("PileUp"))\r
- {\r
- afile = new PileUpfile(inFile, type);\r
- }\r
- else if (format.equals("CLUSTAL"))\r
- {\r
- afile = new ClustalFile(inFile, type);\r
- }\r
- else if (format.equals("BLC"))\r
- {\r
- afile = new BLCFile(inFile, type);\r
- }\r
- else if (format.equals("PIR"))\r
- {\r
- afile = new PIRFile(inFile, type);\r
- }\r
- else if (format.equals("PFAM"))\r
- {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
if (format.equalsIgnoreCase("FASTA"))\r
{\r
afile = new FastaFile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("FASTA_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("MSF"))\r
{\r
- afile = new MSFfile();\r
+ afile = new MSFfile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("MSF_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PileUp"))\r
{\r
afile = new PileUpfile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("PILEUP_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("CLUSTAL"))\r
{\r
afile = new ClustalFile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("CLUSTAL_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("BLC"))\r
{\r
afile = new BLCFile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("BLC_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PIR"))\r
{\r
afile = new PIRFile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("PIR_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PFAM"))\r
{\r
afile = new PfamFile();\r
+ afile.addDBPrefix(\r
+ jalview.bin.Cache.getDefault("PFAM_DBPREFIX", false));\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
}\r
\r
afile.setSeqs(s);\r
maxLength = head.length();\r
}\r
\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
-\r
// Replace ~ with a sensible gap character\r
seq = seq.replace('~', '-');\r
\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
+ Sequence newSeq = parseId(head);\r
+ newSeq.setSequence(seq);\r
\r
seqs.addElement(newSeq);\r
}\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static int checkSum(String seq)\r
+ public int checkSum(String seq)\r
{\r
int check = 0;\r
String sequence = seq.toUpperCase();\r
return check % 10000;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, false);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] seqs, boolean is_NA)\r
+ public String print(SequenceI[] seqs)\r
{\r
\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
+\r
SequenceI [] s = new SequenceI[seqs.length];\r
\r
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii, '~');\r
}\r
else\r
break;\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii,'~');\r
}\r
else\r
break;\r
while ((i < s.length) && (s[i] != null))\r
{\r
\r
- nameBlock[i] = new String(" Name: " + s[i].getName()\r
- + "/" + s[i].getStart() + "-" + s[i].getEnd()\r
- +" ");\r
+ nameBlock[i] = new String(" Name: " + printId(s[i])+" ");\r
\r
idBlock[i] = new String("Len: " +\r
maxLenpad.form(s[i].getSequence().length()) + " Check: " +\r
\r
while ((j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
+ String name = printId( s[j] );\r
\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name+" "));\r
\r
\r
for (int k = 0; k < 5; k++)\r
{\r
try\r
{\r
- String id;\r
- String start;\r
- String end;\r
StringBuffer sequence;\r
String line = null;\r
\r
continue;\r
}\r
\r
- id = "No id";\r
- start = "1";\r
- end = "-1";\r
-\r
- try\r
- {\r
- int slashIndex = line.indexOf("/");\r
- if(slashIndex!=-1)\r
- {\r
- id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
- line = line.substring(line.indexOf("/") + 1);\r
- start = line.substring(0, line.indexOf("-"));\r
- end = line.substring(line.indexOf("-") + 1);\r
- }\r
- else\r
- {\r
- id = line.substring(line.indexOf(";")+1);\r
- }\r
- }\r
- catch (Exception ex)\r
- { }// Default id, start and end unchanged\r
+ Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
\r
sequence = new StringBuffer();\r
\r
- line = nextLine(); // this is the title line\r
+ newSeq.setDescription(nextLine()); // this is the title line\r
\r
boolean starFound = false;\r
\r
{\r
sequence.setLength(sequence.length() - 1);\r
\r
- Sequence newSeq = new Sequence(id, sequence.toString(),\r
- Integer.parseInt(start),\r
- Integer.parseInt(end));\r
+ newSeq.setSequence(sequence.toString());\r
seqs.addElement(newSeq);\r
}\r
}\r
return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, 72, true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len)\r
- {\r
- return print(s, len, true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len, boolean gaps)\r
+ public String print(SequenceI[] s)\r
{\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(s);\r
+ int len = 72;\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String seq = "";\r
+ String seq = s[i].getSequence();\r
+ seq = seq + "*";\r
\r
- if (gaps)\r
- {\r
- seq = s[i].getSequence() + "*";\r
- }\r
+ out.append(">P1;" + printId(s[i]) + "\n");\r
+\r
+ if(s[i].getDescription()!=null)\r
+ out.append(s[i].getDescription()+"\n");\r
else\r
{\r
- seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
- seq = AlignSeq.extractGaps(seq, ".");\r
- seq = AlignSeq.extractGaps(seq, " ");\r
- seq = seq + "*";\r
+ out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));\r
+ out.append( is_NA ? " bases\n" : " residues\n");\r
}\r
-\r
- out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\r
-\r
int nochunks = (seq.length() / len) + 1;\r
\r
for (int j = 0; j < nochunks; j++)\r
public class PfamFile\r
extends AlignFile\r
{\r
- Vector ids;\r
\r
public PfamFile()\r
{\r
public void initData()\r
{\r
super.initData();\r
- ids = new Vector();\r
}\r
\r
public void parse()\r
.length();\r
}\r
\r
- String head = headers.elementAt(i).toString();\r
- int start = 1;\r
- int end = -1;\r
\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = null;\r
-\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString(), start, end);\r
+ Sequence newSeq = parseId(headers.elementAt(i).toString());\r
+ newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());\r
seqs.addElement(newSeq);\r
\r
-\r
if (!isValidProteinSequence(newSeq.getSequence()))\r
{\r
throw new IOException(\r
}\r
}\r
\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("");\r
\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
+ String tmp = printId(s[i]);\r
\r
if (s[i].getSequence().length() > max)\r
{\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
- "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));\r
\r
out.append(s[j].getSequence() + "\n");\r
j++;\r
*\r
**/\r
import java.io.*;\r
-import java.util.*;\r
\r
import jalview.datamodel.*;\r
import jalview.util.*;\r
\r
-public class PileUpfile\r
- extends AlignFile\r
+public class PileUpfile extends MSFfile\r
{\r
- public PileUpfile()\r
- {\r
- }\r
-\r
- public PileUpfile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
\r
- public PileUpfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void parse()\r
- {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
-\r
- try\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ */\r
+ public PileUpfile()\r
{\r
- while ( (line = nextLine()) != null)\r
- {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1)\r
- {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
-\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1)\r
- {\r
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ( (inStr.indexOf("//") == -1) && (seqFlag == true))\r
- {\r
- //seqeunce id is the first field\r
- key = inStr;\r
-\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(key);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens())\r
- {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
}\r
- catch (IOException e)\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inStr)\r
{\r
- System.err.println("Exception parsing PileUpfile " + e);\r
- e.printStackTrace();\r
+ super(inStr);\r
}\r
\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inFile, String type) throws IOException\r
{\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
-\r
- int start = 1;\r
- int end = -1;\r
-\r
- if (maxLength < head.length())\r
- {\r
- maxLength = head.length();\r
- }\r
-\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println(\r
- "PileUpfile Parser: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
+ super(inFile, type);\r
}\r
- }\r
-\r
- public static int checkSum(String seq)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
{\r
-\r
- int check = 0;\r
-\r
- String sequence = seq.toUpperCase();\r
-\r
- for (int i = 0; i < sequence.length(); i++)\r
- {\r
- if (i < sequence.length())\r
- {\r
- int value = sequence.charAt(i);\r
- if (value != -1)\r
- {\r
- check += (i % 57 + 1) * value;\r
- }\r
- }\r
-\r
- }\r
-\r
- return check % 10000;\r
+ return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
+\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("PileUp\n\n");\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
String seq = s[i].getSequence();\r
- out.append(" Name: " + s[i].getName() +\r
- "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+ out.append(" Name: " + printId(s[i]) +\r
" oo Len: " +\r
s[i].getSequence().length() + " Check: " + checksums[i] +\r
" Weight: 1.00\n");\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
+ String name = printId(s[j]);\r
\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name + " "));\r
\r
for (int k = 0; k < 5; k++)\r
{\r
\r
return out.toString();\r
}\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
}\r
\r
import java.util.*;\r
\r
+import org.exolab.castor.mapping.Mapping;\r
+\r
+import org.exolab.castor.xml.*;\r
+import jalview.analysis.AlignSeq;\r
+\r
+\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class SequenceFeatureFetcher implements Runnable\r
{\r
- AlignmentI align;\r
- AlignmentPanel ap;\r
- ArrayList unknownSequences;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- /**\r
- * Creates a new SequenceFeatureFetcher object.\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param ap DOCUMENT ME!\r
- */\r
- public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
+\r
+ AlignmentI align;\r
+ AlignmentPanel ap;\r
+ ArrayList unknownSequences;\r
+ CutAndPasteTransfer output = new CutAndPasteTransfer();\r
+ StringBuffer sbuffer = new StringBuffer();\r
+\r
+ Vector localCache = new Vector();\r
+\r
+ Vector getUniprotEntries(File file)\r
+ {\r
+\r
+ UniprotFile uni = new UniprotFile();\r
+ try\r
{\r
- unknownSequences = new ArrayList();\r
- this.align = align;\r
- this.ap = ap;\r
+ // 1. Load the mapping information from the file\r
+ Mapping map = new Mapping(uni.getClass().getClassLoader());\r
+ java.net.URL url = uni.getClass().getResource("/uniprot_mapping.xml");\r
+ map.loadMapping(url);\r
+\r
+ // 2. Unmarshal the data\r
+ Unmarshaller unmar = new Unmarshaller();\r
+ unmar.setIgnoreExtraElements(true);\r
+ unmar.setMapping(map);\r
+ uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
+ localCache.addAll( uni.getUniprotEntries() );\r
+\r
+ // 3. marshal the data with the total price back and print the XML in the console\r
+ // Marshaller marshaller = new Marshaller(\r
+ // new FileWriter(jalview.bin.Cache.getProperty("UNIPROT_CACHE"))\r
+ // );\r
+ // marshaller.setMapping(map);\r
+ // marshaller.marshal(uni);\r
\r
- Thread thread = new Thread(this);\r
- thread.start();\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
+ catch (Exception e)\r
{\r
- RandomAccessFile out = null;\r
+ System.out.println("Error getUniprotEntries() "+e);\r
+ // e.printStackTrace();\r
+ // if(!updateLocalCache)\r
+ // file.delete();\r
\r
- try\r
- {\r
- String cache = System.getProperty("user.home") +\r
- "/.jalview.uniprot.xml";\r
-\r
- File test = new File(cache);\r
-\r
- if (!test.exists())\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
- out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");\r
- out.writeBytes("<UNIPROT_CACHE>\n");\r
- }\r
- else\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
-\r
- // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
- long lastLine = 0;\r
- String data;\r
-\r
- while ((data = out.readLine()) != null)\r
- {\r
- if (data.indexOf("</entry>") > -1)\r
- {\r
- lastLine = out.getFilePointer();\r
- }\r
- }\r
-\r
- out.seek(lastLine);\r
- }\r
-\r
- int seqIndex = 0;\r
- Vector sequences = align.getSequences();\r
-\r
- while (seqIndex < sequences.size())\r
- {\r
- ArrayList ids = new ArrayList();\r
-\r
- for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
- seqIndex++, i++)\r
- {\r
- SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
- ids.add(sequence.getName());\r
- }\r
-\r
- tryLocalCacheFirst(ids, align);\r
-\r
- if (ids.size() > 0)\r
- {\r
- StringBuffer remainingIds = new StringBuffer("uniprot:");\r
-\r
- for (int i = 0; i < ids.size(); i++)\r
- remainingIds.append(ids.get(i) + ";");\r
-\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData(remainingIds.toString(),\r
- "xml", null);\r
-\r
- if (result != null)\r
- {\r
- ReadUniprotFile(result, out, align);\r
- }\r
- }\r
- }\r
-\r
- if (out != null)\r
- {\r
- out.writeBytes("</UNIPROT_CACHE>\n");\r
- out.close();\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ }\r
+ return uni.getUniprotEntries();\r
+ }\r
+\r
+ /**\r
+ * Creates a new SequenceFeatureFetcher object.\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
+ {\r
+ unknownSequences = new ArrayList();\r
+ this.align = align;\r
+ this.ap = ap;\r
+\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ int seqIndex = 0;\r
+ Vector sequences = align.getSequences();\r
\r
- findMissingIds(align);\r
+ while (seqIndex < sequences.size())\r
+ {\r
+ Vector ids = new Vector();\r
\r
- if (sbuffer.length() > 0)\r
+ for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
+ seqIndex++, i++)\r
{\r
- output.setText(\r
- "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
- "altered, most likely the start/end residue will have been updated.\n" +\r
- "Save your alignment to maintain the updated id.\n\n" +\r
- sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
+ SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
+ ids.add(sequence.getName());\r
+ unknownSequences.add(sequence.getName());\r
}\r
\r
- if (unknownSequences.size() > 0)\r
+ ///////////////////////////////////\r
+ ///READ FROM EBI\r
+ if (ids.size() > 0)\r
{\r
- //ignore for now!!!!!!!!!!\r
- // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
+ StringBuffer remainingIds = new StringBuffer("uniprot:");\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ remainingIds.append(ids.get(i) + ";");\r
+ }\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ File file = ebi.fetchDataAsFile(remainingIds.toString(),\r
+ "xml", null);\r
+\r
+\r
+ if (file != null)\r
+ {\r
+ ReadUniprotFile(file, align, ids);\r
+ }\r
}\r
-\r
- jalview.gui.PaintRefresher.Refresh(null, align);\r
+ }\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param result DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)\r
+ catch (Exception ex)\r
{\r
- SequenceI sequence = null;\r
- Vector features = null;\r
- String type;\r
- String description;\r
- String status;\r
- String start;\r
- String end;\r
- String pdb = null;\r
-\r
- for (int r = 0; r < result.length; r++)\r
- {\r
- if ((sequence == null) && (result[r].indexOf("<name>") > -1))\r
- {\r
- long filePointer = 0;\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- filePointer = out.getFilePointer();\r
- out.writeBytes("<entry>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- String seqName = parseElement(result[r], "<name>", out);\r
- sequence = align.findName(seqName);\r
-\r
- if (sequence == null)\r
- {\r
- sequence = align.findName(seqName.substring(0,\r
- seqName.indexOf('_')));\r
-\r
- if (sequence != null)\r
- {\r
- sbuffer.append("changing " + sequence.getName() +\r
- " to " + seqName + "\n");\r
- sequence.setName(seqName);\r
- }\r
- }\r
-\r
- if (sequence == null)\r
- {\r
- sbuffer.append("UNIPROT updated suggestion is " +\r
- result[r] + "\n");\r
- sequence = align.findName(result[r]);\r
-\r
- // this entry has been suggested by ebi.\r
- // doesn't match id in alignment file\r
- try\r
- {\r
- out.setLength(filePointer);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- // now skip to next entry\r
- while (result[r].indexOf("</entry>") == -1)\r
- r++;\r
- }\r
-\r
- features = new Vector();\r
- type = "";\r
- start = "0";\r
- end = "0";\r
- description = "";\r
- status = "";\r
- pdb = "";\r
- }\r
-\r
- if (sequence == null)\r
- {\r
- continue;\r
- }\r
-\r
- if (result[r].indexOf("<property type=\"pdb accession\"") > -1)\r
- {\r
- pdb = parseValue(result[r], "value=", out);\r
- sequence.setPDBId(pdb);\r
- }\r
-\r
- if (result[r].indexOf("feature type") > -1)\r
- {\r
- type = parseValue(result[r], "type=", out);\r
- description = parseValue(result[r], "description=", null);\r
- status = parseValue(result[r], "status=", null);\r
-\r
- while (result[r].indexOf("position") == -1)\r
- {\r
- r++; //<location>\r
- }\r
-\r
- // r++;\r
- if (result[r].indexOf("begin") > -1)\r
- {\r
- start = parseValue(result[r], "position=", out);\r
- end = parseValue(result[++r], "position=", out);\r
- }\r
- else\r
- {\r
- start = parseValue(result[r], "position=", out);\r
- end = parseValue(result[r], "position=", null);\r
- }\r
-\r
- int sstart = Integer.parseInt(start);\r
- int eend = Integer.parseInt(end);\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes("</feature>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- SequenceFeature sf = new SequenceFeature(type, sstart, eend,\r
- description, status);\r
- features.add(sf);\r
- }\r
-\r
- if (result[r].indexOf("<sequence length=") > -1)\r
- {\r
- StringBuffer seqString = new StringBuffer();\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- while (result[++r].indexOf("</sequence>") == -1)\r
- {\r
- seqString.append(result[r]);\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- StringBuffer nonGapped = new StringBuffer();\r
-\r
- for (int i = 0; i < sequence.getSequence().length(); i++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
- {\r
- nonGapped.append(sequence.getCharAt(i));\r
- }\r
- }\r
-\r
- int absStart = seqString.toString().indexOf(nonGapped.toString());\r
-\r
- if (absStart == -1)\r
- {\r
- unknownSequences.add(sequence.getName());\r
- features = null;\r
- sbuffer.append(sequence.getName() +\r
- " SEQUENCE NOT %100 MATCH \n");\r
-\r
- continue;\r
- }\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart += 1;\r
-\r
- if ((absStart != sequence.getStart()) ||\r
- (absEnd != sequence.getEnd()))\r
- {\r
- sbuffer.append("Updated: " + sequence.getName() + " " +\r
- sequence.getStart() + "/" + sequence.getEnd() +\r
- " to " + absStart + "/" + absEnd + "\n");\r
- }\r
-\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
- }\r
-\r
- if (result[r].indexOf("</entry>") > -1)\r
- {\r
- if (features != null)\r
- {\r
- sequence.setSequenceFeatures(features);\r
- }\r
-\r
- features = null;\r
- sequence = null;\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes("</entry>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
- }\r
+ ex.printStackTrace();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param align DOCUMENT ME!\r
- */\r
- void findMissingIds(AlignmentI align)\r
+ if (sbuffer.length() > 0)\r
{\r
- String data;\r
- ArrayList cachedIds = new ArrayList();\r
-\r
- try\r
- {\r
- if(jalview.bin.Cache.getProperty("UNIPROT_CACHE")==null)\r
- return;\r
-\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (data.indexOf("name") > -1)\r
- {\r
- String name = parseElement(data, "<name>", null);\r
- cachedIds.add(name);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- for (int i = 0; i < align.getHeight(); i++)\r
- if (!cachedIds.contains(align.getSequenceAt(i).getName()))\r
- {\r
- unknownSequences.add(align.getSequenceAt(i).getName());\r
- }\r
+ output.setText(\r
+ "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
+ "altered, most likely the start/end residue will have been updated.\n" +\r
+ "Save your alignment to maintain the updated id.\n\n" +\r
+ sbuffer.toString());\r
+ Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ids DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void tryLocalCacheFirst(ArrayList ids, AlignmentI align)\r
+ if (unknownSequences.size() > 0)\r
{\r
- ArrayList cacheData = new ArrayList();\r
-\r
- try\r
- {\r
- if(jalview.bin.Cache.getProperty("UNIPROT_CACHE")==null)\r
- return;\r
-\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\r
- // read through cache file, if the cache has sequences we're looking for\r
- // add the lines to a new String array, Readthis new array and\r
- // make sure we remove the ids from the list to retrieve from EBI\r
- String data;\r
-\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (data.indexOf("name") > -1)\r
- {\r
- String name = parseElement(data, "<name>", null);\r
-\r
- if (ids.contains(name))\r
- {\r
- cacheData.add("<entry>");\r
- cacheData.add(data);\r
-\r
- while (data.indexOf("</entry>") == -1)\r
- {\r
- data = in.readLine();\r
- cacheData.add(data);\r
- }\r
-\r
- cacheData.add(data);\r
-\r
- ids.remove(name);\r
- }\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- String[] localData = new String[cacheData.size()];\r
- cacheData.toArray(localData);\r
-\r
- if ((localData != null) && (localData.length > 0))\r
- {\r
- ReadUniprotFile(localData, null, align);\r
- }\r
+ new WSWUBlastClient(ap, align, unknownSequences);\r
}\r
+ else\r
+ ((Alignment)align).featuresAdded = true;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param line DOCUMENT ME!\r
- * @param tag DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- String parseValue(String line, String tag, RandomAccessFile out)\r
- {\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
\r
- int index = line.indexOf(tag) + tag.length() + 1;\r
+ ap.repaint();\r
+ }\r
\r
- if (index == tag.length())\r
- {\r
- return "";\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param result DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ void ReadUniprotFile(File file, AlignmentI align, Vector ids)\r
+ {\r
+ if(!file.exists())\r
+ return;\r
\r
- return line.substring(index, line.indexOf("\"", index + 1));\r
- }\r
+ SequenceI sequence = null;\r
+ // String pdb = null;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param line DOCUMENT ME!\r
- * @param tag DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- String parseElement(String line, String tag, RandomAccessFile out)\r
- {\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- int index = line.indexOf(tag) + tag.length();\r
+ Vector entries = getUniprotEntries(file);\r
\r
- return line.substring(index, line.indexOf("</"));\r
+ int i, iSize = entries==null?0:entries.size();\r
+ UniprotEntry entry;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ entry = (UniprotEntry) entries.elementAt(i);\r
+ String idmatch = entry.getAccession();\r
+ sequence = align.findName(idmatch);\r
+\r
+ if (sequence == null)\r
+ {\r
+ //Sequence maybe Name, not Accession\r
+ idmatch = entry.getName();\r
+ sequence = align.findName(idmatch);\r
+ }\r
+\r
+ if (sequence == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ ids.remove(sequence.getName());\r
+ unknownSequences.remove(sequence.getName());\r
+\r
+ String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());\r
+\r
+ int absStart = entry.getUniprotSequence().getContent().indexOf(\r
+ nonGapped.toString());\r
+\r
+ if (absStart == -1)\r
+ {\r
+ unknownSequences.add(sequence.getName());\r
+ sbuffer.append(sequence.getName() +\r
+ " SEQUENCE NOT %100 MATCH \n");\r
+\r
+ continue;\r
+ }\r
+\r
+ int absEnd = absStart + nonGapped.toString().length();\r
+ absStart += 1;\r
+\r
+ if ( (absStart != sequence.getStart()) ||\r
+ (absEnd != sequence.getEnd()))\r
+ {\r
+ sbuffer.append("Updated: " + sequence.getName() + " " +\r
+ sequence.getStart() + "/" + sequence.getEnd() +\r
+ " to " + absStart + "/" + absEnd + "\n");\r
+ }\r
+\r
+ sequence.setSequenceFeatures(entry.getFeatures());\r
+ sequence.setStart(absStart);\r
+ sequence.setEnd(absEnd);\r
}\r
+ }\r
}\r
+\r
+\r
--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ */\r
+\r
+package jalview.io;\r
+\r
+import org.vamsas.objects.core.*;\r
+\r
+import jalview.gui.*;\r
+import java.io.*;\r
+import java.util.jar.*;\r
+\r
+/*\r
+\r
+ static {\r
+ org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(\r
+ "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer");\r
+ }\r
+\r
+*/\r
+\r
+public class VamsasDatastore\r
+{\r
+ AlignViewport av;\r
+ org.exolab.castor.types.Date date\r
+ = new org.exolab.castor.types.Date(new java.util.Date());\r
+\r
+ public VamsasDatastore(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+ public void store(String file)\r
+ {\r
+ storeVAMSAS(file);\r
+ }\r
+\r
+\r
+\r
+ public VAMSAS storeVAMSAS(String file)\r
+ {\r
+ long time = System.currentTimeMillis();\r
+ VAMSAS vamsas = new VAMSAS();\r
+\r
+ try\r
+ {\r
+ FileOutputStream fos = new FileOutputStream(file);\r
+ JarOutputStream jout = new JarOutputStream(fos);\r
+\r
+\r
+ ////////////////////////////////////////////////////\r
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
+ "UTF-8"));\r
+\r
+ jalview.datamodel.AlignmentI jal = av.getAlignment();\r
+\r
+\r
+ ///////////////////////////////////////////\r
+ // SAVE THE DATASET\r
+ DataSet dataset = new DataSet();\r
+ vamsas.addDataSet(dataset);\r
+\r
+ Sequence sequence;\r
+ DbRef dbref;\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
+ {\r
+ sequence = new Sequence();\r
+ sequence.setSequence(jal.getDataset().getSequenceAt(i).getSequence());\r
+ sequence.setName(jal.getDataset().getSequenceAt(i).getName());\r
+ sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());\r
+ sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());\r
+\r
+ if(jal.getDataset().getSequenceAt(i).getDBRef()!=null)\r
+ {\r
+ java.util.Vector entries = jal.getDataset().getSequenceAt(i).getDBRef();\r
+ jalview.datamodel.DBRefEntry dbentry;\r
+ for(int db=0; db<entries.size(); db++)\r
+ {\r
+ dbentry = (jalview.datamodel.DBRefEntry)entries.elementAt(db);\r
+ dbref = new DbRef();\r
+ dbref.setAccessionId( dbentry.getAccessionId() );\r
+ dbref.setSource( dbentry.getSource() );\r
+ dbref.setVersion( dbentry.getVersion() );\r
+ dbref.setId("db"+(time++));\r
+ sequence.addDbRef(dbref);\r
+ }\r
+\r
+ }\r
+\r
+\r
+ if(jal.getDataset().getSequenceAt(i).getVamsasId()==null)\r
+ sequence.setId("ds" + (time++));\r
+ else\r
+ sequence.setId(jal.getDataset().getSequenceAt(i).getVamsasId());\r
+\r
+ dataset.addSequence(sequence);\r
+ }\r
+ dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));\r
+ //////////////////////////////////////////////\r
+\r
+\r
+ //////////////////////////////////////////////\r
+ //Save the Alignments\r
+ Alignment alignment = new Alignment();\r
+ alignment.setGapChar(av.getGapCharacter() + "");\r
+ AlignmentSequence alseq = null;\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
+ {\r
+ alseq = new AlignmentSequence();\r
+ alseq.setSequence(\r
+ jal.getSequenceAt(i).getSequence()\r
+ );\r
+ alseq.setName(jal.getSequenceAt(i).getName());\r
+ alseq.setStart(jal.getSequenceAt(i).getStart());\r
+ alseq.setEnd(jal.getSequenceAt(i).getEnd());\r
+ alseq.setRefid(dataset.getSequence(i));\r
+ alseq.setId("as" + (time++));\r
+ alignment.addAlignmentSequence(alseq);\r
+ }\r
+ alignment.setProvenance(getVamsasProvenance(jal.getProvenance()));\r
+ dataset.addAlignment(alignment);\r
+ //////////////////////////////////////////////\r
+\r
+\r
+\r
+ //////////////////////////////////////////////\r
+ //SAVE ANNOTATIONS\r
+ if (jal.getAlignmentAnnotation() != null)\r
+ {\r
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].label.equals("Quality") ||\r
+ aa[i].label.equals("Conservation") ||\r
+ aa[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ AlignmentAnnotations an = new AlignmentAnnotations();\r
+\r
+ an.setDescription(aa[i].description);\r
+ an.setGraph(aa[i].isGraph);\r
+ an.setLabel(aa[i].label);\r
+ an.setProvenance(dummyProvenance());\r
+\r
+ AnnotationElement ae;\r
+\r
+ for (int a = 0; a < aa[i].annotations.length; a++)\r
+ {\r
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ ae = new AnnotationElement();\r
+ ae.setDescription(aa[i].annotations[a].description);\r
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
+ ae.setValue(aa[i].annotations[a].value);\r
+ ae.setPosition(a);\r
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
+ "");\r
+ an.addAnnotationElement(ae);\r
+ }\r
+\r
+ alignment.addAlignmentAnnotations(an);\r
+ }\r
+ }\r
+ ///////////////////////////////////////////////////////\r
+\r
+\r
+ ////////////////////////////////////////////////\r
+ ///SAVE THE TREES\r
+ ///////////////////////////////////\r
+ // FIND ANY ASSOCIATED TREES\r
+ if (Desktop.desktop != null)\r
+ {\r
+ javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ for (int t = 0; t < frames.length; t++)\r
+ {\r
+ if (frames[t] instanceof TreePanel)\r
+ {\r
+ TreePanel tp = (TreePanel) frames[t];\r
+\r
+ if (tp.getAlignment() == jal)\r
+ {\r
+ Tree tree = new Tree();\r
+ tree.setTitle(tp.getTitle());\r
+ Newick newick = new Newick();\r
+ newick.setContent( tp.getTree().toString() );\r
+ newick.setTitle( tp.getTitle() );\r
+ newick.setId("t"+(time++));\r
+ tree.addNewick( newick );\r
+ tree.setProvenance(dummyProvenance());\r
+ alignment.addTree(tree);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ JarEntry entry = new JarEntry("vamsas.xml");\r
+ jout.putNextEntry(entry);\r
+\r
+ vamsas.marshal(out);\r
+\r
+ out.close();\r
+ jout.close();\r
+\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return vamsas;\r
+ }\r
+\r
+ Tree jalview2VamsasTree()\r
+ {\r
+ Tree tree = new Tree();\r
+\r
+ return tree;\r
+ }\r
+\r
+\r
+ public void load(String file)\r
+ {\r
+ VAMSAS vamsas = new VAMSAS() ;\r
+\r
+ try\r
+ {\r
+ FileInputStream fis = new FileInputStream(file);\r
+ JarInputStream jin = new JarInputStream(fis);\r
+\r
+\r
+ ////////////////////////////////////////////////////\r
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
+ JarEntry jarentry = jin.getNextJarEntry();\r
+ System.out.println("reading: "+jarentry.getName());\r
+ vamsas = (VAMSAS) vamsas.unmarshal(in);\r
+\r
+\r
+ /////////////////////////////////////\r
+ /////LOAD DATASET\r
+ DataSet dataset = vamsas.getDataSet(0);\r
+\r
+ int i, iSize = dataset.getSequenceCount();\r
+ jalview.datamodel.Sequence [] seqs = new jalview.datamodel.Sequence[iSize];\r
+ DbRef [] dbref;\r
+\r
+ for (i = 0; i < iSize ; i++)\r
+ {\r
+ seqs[i] = new jalview.datamodel.Sequence(\r
+ dataset.getSequence(i).getName(),\r
+ dataset.getSequence(i).getSequence(),\r
+ dataset.getSequence(i).getStart(),\r
+ dataset.getSequence(i).getEnd() );\r
+ seqs[i].setVamsasId(dataset.getSequence(i).getId());\r
+\r
+ dbref = dataset.getSequence(i).getDbRef();\r
+\r
+ if(dbref.length>0)\r
+ {\r
+ for(int db=0; db<dbref.length; db++)\r
+ {\r
+ seqs[i].addDBRef( new jalview.datamodel.DBRefEntry\r
+ (\r
+ dbref[db].getSource().toString(),\r
+ dbref[db].getVersion().toString(),\r
+ dbref[db].getAccessionId().toString()));\r
+ }\r
+ }\r
+\r
+ }\r
+ jalview.datamodel.Alignment jdataset = new jalview.datamodel.Alignment(seqs);\r
+ ////////////////////////////////////////////////\r
+\r
+\r
+ //////////////////////////////////////\r
+ ////LOAD ALIGNMENT\r
+ Alignment alignment = dataset.getAlignment(0);\r
+ iSize = alignment.getAlignmentSequenceCount();\r
+ seqs = new jalview.datamodel.Sequence[iSize];\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ seqs[i] = new jalview.datamodel.Sequence(\r
+ alignment.getAlignmentSequence(i).getName(),\r
+ alignment.getAlignmentSequence(i).getSequence(),\r
+ alignment.getAlignmentSequence(i).getStart(),\r
+ alignment.getAlignmentSequence(i).getEnd());\r
+ }\r
+ jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);\r
+ jal.setDataset(jdataset);\r
+ jal.getDataset().setProvenance(\r
+ getJalviewProvenance(dataset.getProvenance()));\r
+ jal.setProvenance(\r
+ getJalviewProvenance(alignment.getProvenance()));\r
+ //////////////////////////////////////////////\r
+\r
+\r
+ ////////////////////////////////////////////\r
+ ////LOAD ANNOTATIONS\r
+ ////////////////////\r
+ if (alignment.getAlignmentAnnotationsCount()>0)\r
+ {\r
+ AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();\r
+\r
+ for (int j = 0; j < an.length; j++)\r
+ {\r
+ boolean topaliBreakpoint = false;\r
+\r
+ AnnotationElement[] ae = an[j].getAnnotationElement();\r
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[jal.\r
+ getWidth()];\r
+\r
+ try{\r
+\r
+ for (int aa = 0; aa < ae.length; aa++)\r
+ {\r
+ String dc = ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();\r
+ String desc = ae[aa].getDescription()==null ? "desc" : ae[aa].getDescription();\r
+ String ss = ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();\r
+ float value = ae[aa].getValue();\r
+\r
+ if(an[j].getGraph())\r
+ {\r
+ dc = value+"";\r
+ desc = value + "";\r
+ }\r
+ anot[ae[aa].getPosition()-1] = new jalview.datamodel.\r
+ Annotation(dc,desc,ss.charAt(0),value);\r
+\r
+ if(desc.equals("TOPALi Partition Breakpoint"))\r
+ topaliBreakpoint = true;\r
+\r
+ }\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("problem parsing annotations\n"+ex);}\r
+\r
+ jalview.datamodel.AlignmentAnnotation jaa = null;\r
+\r
+ if (an[j].getGraph())\r
+ {\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[j].getLabel(),\r
+ an[j].getDescription(), anot, 0, 0, 1);\r
+ }\r
+ else\r
+ {\r
+ String label = an[j].getLabel();\r
+ if(topaliBreakpoint)\r
+ label = "TOPALi Partition Breakpoint";\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(label,\r
+ an[j].getDescription(), anot);\r
+ }\r
+\r
+ jal.addAnnotation(jaa);\r
+ }\r
+ }\r
+ /////////////////////////////////\r
+\r
+ AlignFrame alignFrame = new AlignFrame(jal);\r
+ jalview.gui.Desktop.addInternalFrame(alignFrame, "VAMSAS LOAD",\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+\r
+ //LOAD TREES\r
+ ///////////////////////////////////////\r
+ if (alignment.getTreeCount() > 0)\r
+ {\r
+ for (int t = 0; t < alignment.getTreeCount(); t++)\r
+ {\r
+ Tree tree = alignment.getTree(t);\r
+\r
+ alignFrame.ShowNewickTree(\r
+ new jalview.io.NewickFile(tree.getNewick(0).getContent()),\r
+ tree.getNewick(0).getTitle(),\r
+ 600, 500,\r
+ t * 20 + 50, t * 20 + 50);\r
+ }\r
+ }\r
+\r
+\r
+ in.close();\r
+ jin.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+\r
+ }\r
+\r
+\r
+\r
+ Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov)\r
+ {\r
+ jalview.datamodel.ProvenanceEntry [] entries = null;\r
+\r
+\r
+ Provenance prov = new Provenance();\r
+ org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
+ new java.util.Date());\r
+ Entry provEntry;\r
+\r
+ if(jprov!=null)\r
+ {\r
+ entries = jprov.getEntries();\r
+ for (int i = 0; i < entries.length; i++)\r
+ {\r
+ provEntry = new Entry();\r
+ try\r
+ {\r
+ date = new org.exolab.castor.types.Date(entries[i].getDate());\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+\r
+ date = new org.exolab.castor.types.Date(entries[i].getDate());\r
+ }\r
+ provEntry.setDate(date);\r
+ provEntry.setUser(entries[i].getUser());\r
+ provEntry.setAction(entries[i].getAction());\r
+ prov.addEntry(provEntry);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ provEntry = new Entry();\r
+ provEntry.setDate(date);\r
+ provEntry.setUser(System.getProperty("user.name"));\r
+ provEntry.setAction("Jalview");\r
+ prov.addEntry(provEntry);\r
+ }\r
+\r
+ return prov;\r
+ }\r
+\r
+ jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)\r
+ {\r
+\r
+ jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();\r
+ for (int i = 0; i < prov.getEntryCount(); i++)\r
+ {\r
+ jprov.addEntry(\r
+ prov.getEntry(i).getUser(),\r
+ prov.getEntry(i).getAction(),\r
+ prov.getEntry(i).getDate().toDate(),\r
+ prov.getEntry(i).getId()\r
+ );\r
+ }\r
+\r
+ return jprov;\r
+ }\r
+\r
+ Provenance dummyProvenance()\r
+ {\r
+ Provenance prov = new Provenance();\r
+ Entry entry = new Entry();\r
+ entry.setAction("Jalview");\r
+ entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
+ entry.setUser(System.getProperty("user.name"));\r
+ prov.addEntry(entry);\r
+ return prov;\r
+ }\r
+\r
+}\r
*/\r
public class WSWUBlastClient\r
{\r
+ AlignmentPanel ap;\r
+ AlignmentI al;\r
CutAndPasteTransfer output = new CutAndPasteTransfer();\r
int jobsRunning = 0;\r
\r
+ Hashtable suggestedIds = new Hashtable();\r
/**\r
* Creates a new WSWUBlastClient object.\r
*\r
* @param al DOCUMENT ME!\r
* @param ids DOCUMENT ME!\r
*/\r
- public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
+ public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)\r
{\r
+ this.ap = ap;\r
+ this.al = al;\r
output.setText(\r
"To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
SequenceI sequence = al.findName(ids.get(i).toString());\r
StringBuffer nonGapped = new StringBuffer();\r
\r
+\r
for (int n = 0; n < sequence.getSequence().length(); n++)\r
{\r
if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
thread.start();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
data = st.nextToken();\r
\r
- if (data.indexOf("database=\"uniprot\" id=") > -1)\r
+ if (data.indexOf(">UNIPROT") > -1)\r
{\r
- int index = data.indexOf("database=\"uniprot\" id=") + 23;\r
- id2 = data.substring(index, data.indexOf("\"", index));\r
+ int index = data.indexOf(">UNIPROT") + 9;\r
+ id2 = data.substring(index, data.indexOf(" ", index));\r
\r
- while (data.indexOf("</alignment>") == -1)\r
+ boolean identitiesFound = false;\r
+ while (!identitiesFound)\r
{\r
data = st.nextToken();\r
\r
- if (data.indexOf("<identity>") > -1)\r
+ if (data.indexOf("Identities") > -1)\r
{\r
- int value = Integer.parseInt(data.substring(data.indexOf(\r
- "<identity>") + 10,\r
- data.indexOf("</identity>")));\r
+ identitiesFound = true;\r
+\r
+ int value = Integer.parseInt(data.substring(data.indexOf(\r
+ "(") + 1,\r
+ data.indexOf("%")));\r
\r
if (value >= maxFound)\r
{\r
maxFound = value;\r
buffer.append(" " + id2 + " " + value + "%; ");\r
+ suggestedIds.put(id1, id2);\r
}\r
}\r
}\r
}\r
}\r
\r
- output.setText(output.getText() + buffer.toString());\r
+ output.appendText(buffer.toString());\r
+ }\r
+\r
+ void updateIds()\r
+ {\r
+\r
}\r
\r
class ImageTwirler extends Thread\r
{\r
}\r
}\r
+\r
+ if (jobsRunning == 0)\r
+ {\r
+ int reply = JOptionPane.showConfirmDialog(\r
+ Desktop.desktop, "Automatically update suggested ids?",\r
+ "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ {\r
+ Enumeration keys = suggestedIds.keys();\r
+ while(keys.hasMoreElements())\r
+ {\r
+ String oldid = keys.nextElement().toString();\r
+ SequenceI sequence = al.findName(oldid);\r
+ sequence.setName( suggestedIds.get(oldid).toString() );\r
+\r
+ sequence = al.getDataset().findName(oldid);\r
+ Vector entries = sequence.getDBRef();\r
+ DBRefEntry entry = (DBRefEntry) entries.elementAt(0);\r
+ sequence.addDBRef(new jalview.datamodel.DBRefEntry("UNIPROT",\r
+ "0",\r
+ entry.getAccessionId()));\r
+\r
+ sequence.setName(suggestedIds.get(oldid).toString());\r
+\r
+ System.out.println("replace "+oldid+" with "+suggestedIds.get(oldid));\r
+ }\r
+ }\r
+ ap.repaint();\r
+ }\r
}\r
}\r
\r
\r
BlastThread(String id, String sequence)\r
{\r
+ System.out.println("blasting for: "+id);\r
this.sequence = sequence;\r
seqid = id;\r
}\r
"http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
call.setOperationName(new QName("WSWUBlast", "polljob"));\r
\r
- String result = (String) call.invoke(new Object[]\r
+ Object object = (String) call.invoke(new Object[]\r
{\r
jobid, "xml"\r
});\r
\r
- if ((result.indexOf("JOB PENDING") == -1) &&\r
- (result.indexOf("JOB RUNNING") == -1))\r
+ if(object instanceof String)\r
{\r
- parseResult(seqid, result);\r
- jobComplete = true;\r
- jobsRunning--;\r
+ parseResult(seqid, (String)object);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
}\r
\r
Thread.sleep(5000);\r
\r
- // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
+ System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
}\r
catch (Exception ex)\r
{\r
params.put("matrix", "pam10");\r
params.put("program", "blastp");\r
params.put("alignments", "5");\r
- params.put("outformat", "xml");\r
- params.put("searchtype", "1");\r
+ params.put("type", "xml");\r
+ params.put("async", "true");\r
\r
byte[] seqbytes = sequence.getBytes();\r
\r
"http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
\r
- String result = (String) call.invoke(new Object[]\r
+ Object object = call.invoke(new Object[]\r
{\r
params, seqbytes\r
});\r
- jobid = result;\r
- System.out.println(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
- jobid + "'");\r
+\r
+ if(object instanceof byte[])\r
+ jobid = new String( (byte[])object);\r
+\r
+ else\r
+ {\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ parseResult(seqid, (String)object);\r
+ }\r
+\r
}\r
catch (Exception exp)\r
{\r
MenuItem item;\r
\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) {\r
+ item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(\r
i));\r
item.addActionListener(new java.awt.event.ActionListener() {\r
public void actionPerformed(ActionEvent e) {\r
}\r
});\r
\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(\r
i));\r
item.addActionListener(new java.awt.event.ActionListener() {\r
public void actionPerformed(ActionEvent e) {\r
JMenu jMenu2 = new JMenu();\r
JMenuItem padGapsMenuitem = new JMenuItem();\r
protected ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ protected JTabbedPane tabbedPane = new JTabbedPane();\r
+ protected JMenuItem featureSettings = new JMenuItem();\r
\r
public GAlignFrame()\r
{\r
padGapsMenuitem_actionPerformed(e);\r
}\r
});\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasStore_actionPerformed(e);\r
+ }\r
+ });\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showTranslation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ tabbedPane.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent ece)\r
+ {\r
+\r
+ tabSelected();\r
+ }\r
+ });\r
+// featureSettings.setEnabled(false);\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ featureSettings_actionPerformed(e);\r
+ }\r
+ });\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(webService);\r
+ fileMenu.add(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\r
colourMenu.add(applyToAllGroups);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(showTranslation);\r
webServiceNoServices=new JMenuItem("<No Services>");\r
webService.add(webServiceNoServices);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
jMenu1.add(pasteNew);\r
jMenu1.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
protected void ClustalRealign_actionPerformed(ActionEvent e)\r
{\r
}\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void tabSelected()\r
+ {\r
+\r
+ }\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
JMenuItem saveState = new JMenuItem();\r
JMenuItem loadState = new JMenuItem();\r
JMenu jMenu1 = new JMenu();\r
+ JMenuItem vamsasLoad = new JMenuItem();\r
\r
- /**\r
+ /**\r
* Creates a new GDesktop object.\r
*/\r
public GDesktop()\r
});\r
jMenu1.setMnemonic('I');\r
jMenu1.setText("Input Alignment");\r
- DesktopMenubar.add(FileMenu);\r
+ vamsasLoad.setText("Vamsas");\r
+ vamsasLoad.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasLoad_actionPerformed(e);\r
+ }\r
+ });\r
+ DesktopMenubar.add(FileMenu);\r
DesktopMenubar.add(toolsMenu);\r
DesktopMenubar.add(HelpMenu);\r
DesktopMenubar.add(windowMenu);\r
jMenu1.add(inputLocalFileMenuItem);\r
jMenu1.add(inputURLMenuItem);\r
jMenu1.add(inputTextboxMenuItem);\r
- }\r
+ jMenu1.add(vamsasLoad);\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
{\r
}\r
+\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
protected JCheckBox useProxy = new JCheckBox();\r
JPanel jPanel1 = new JPanel();\r
TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
+ TitledBorder titledBorder2 = new TitledBorder("File Output");\r
GridBagLayout gridBagLayout2 = new GridBagLayout();\r
GridBagLayout gridBagLayout1 = new GridBagLayout();\r
GridBagLayout gridBagLayout3 = new GridBagLayout();\r
JPanel exportTab = new JPanel();\r
JLabel epsLabel = new JLabel();\r
protected JComboBox epsRendering = new JComboBox();\r
+ JLabel jLabel1 = new JLabel();\r
+ JLabel jLabel2 = new JLabel();\r
+ protected JCheckBox pileupdb = new JCheckBox();\r
+ protected JCheckBox fastadb = new JCheckBox();\r
+ protected JCheckBox blcjv = new JCheckBox();\r
+ protected JCheckBox pileupjv = new JCheckBox();\r
+ protected JCheckBox msfdb = new JCheckBox();\r
+ protected JCheckBox pfamdb = new JCheckBox();\r
+ protected JCheckBox clustaljv = new JCheckBox();\r
+ protected JCheckBox msfjv = new JCheckBox();\r
+ protected JCheckBox blcdb = new JCheckBox();\r
+ protected JCheckBox clustaldb = new JCheckBox();\r
+ protected JCheckBox fastajv = new JCheckBox();\r
+ protected JCheckBox pfamjv = new JCheckBox();\r
+ JLabel jLabel10 = new JLabel();\r
+ JLabel jLabel11 = new JLabel();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ protected JCheckBox pirdb = new JCheckBox();\r
+ protected JCheckBox pirjv = new JCheckBox();\r
+ JPanel jPanel11 = new JPanel();\r
+ GridLayout gridLayout3 = new GridLayout();\r
+ Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
/**\r
* Creates a new GPreferences object.\r
*/\r
}\r
});\r
quality.setEnabled(false);\r
- quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ quality.setFont(verdana11);\r
quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
quality.setSelected(true);\r
quality.setText("Quality");\r
visualTab.setBorder(new TitledBorder("Open new alignment"));\r
visualTab.setLayout(null);\r
- fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fullID.setFont(verdana11);\r
fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
fullID.setMargin(new Insets(4, 2, 2, 0));\r
fullID.setText("Full Sequence ID");\r
- fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fullScreen.setFont(verdana11);\r
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
fullScreen.setMargin(new Insets(2, 2, 2, 0));\r
fullScreen.setText("Maximise Window");\r
conservation.setEnabled(false);\r
- conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ conservation.setFont(verdana11);\r
conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
conservation.setSelected(true);\r
conservation.setText("Conservation");\r
identity.setEnabled(false);\r
- identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ identity.setFont(verdana11);\r
identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
identity.setSelected(true);\r
identity.setText("Consensus");\r
- annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ annotations.setFont(verdana11);\r
annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
annotations.setMargin(new Insets(2, 4, 2, 0));\r
annotations_actionPerformed(e);\r
}\r
});\r
- gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ gapLabel.setFont(verdana11);\r
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
gapLabel.setText("Gap Symbol ");\r
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ colour.setFont(verdana11);\r
colour.setBounds(new Rectangle(148, 171, 154, 21));\r
- colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ colourLabel.setFont(verdana11);\r
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
colourLabel.setText("Colour ");\r
- fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontLabel.setFont(verdana11);\r
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
fontLabel.setText("Font ");\r
- fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontSizeCB.setFont(verdana11);\r
fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));\r
- fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontStyleCB.setFont(verdana11);\r
fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
- fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontNameCB.setFont(verdana11);\r
fontNameCB.setBounds(new Rectangle(148, 111, 169, 21));\r
- gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ gapSymbolCB.setFont(verdana11);\r
gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21));\r
startupCheckbox.setText("Open file");\r
- startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ startupCheckbox.setFont(verdana11);\r
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
startupCheckbox.setSelected(true);\r
- startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ startupFileTextfield.setFont(verdana11);\r
startupFileTextfield.setBounds(new Rectangle(148, 232, 302, 20));\r
startupFileTextfield.addMouseListener(new MouseAdapter()\r
{\r
connectTab.setLayout(gridBagLayout3);\r
serverLabel.setText("Address");\r
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- serverLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyServerTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyPortTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- portLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ serverLabel.setFont(verdana11);\r
+ proxyServerTB.setFont(verdana11);\r
+ proxyPortTB.setFont(verdana11);\r
+ portLabel.setFont(verdana11);\r
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
portLabel.setText("Port");\r
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
browserLabel.setText("Default Browser (Unix)");\r
- defaultBrowser.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ defaultBrowser.setFont(verdana11);\r
defaultBrowser.setText("");\r
newLink.setText("New");\r
newLink.addActionListener(new java.awt.event.ActionListener() {\r
linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
linkPanel2.setLayout(borderLayout3);\r
- linkURLList.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ linkURLList.setFont(verdana11);\r
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
\r
defaultBrowser.addMouseListener(new MouseAdapter()\r
}\r
}\r
});\r
- useProxy.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ useProxy.setFont(verdana11);\r
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
useProxy.setText("Use a proxy server");\r
});\r
jPanel1.setBorder(titledBorder1);\r
jPanel1.setLayout(gridBagLayout1);\r
- sortby.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ sortby.setFont(verdana11);\r
sortby.setBounds(new Rectangle(148, 200, 302, 21));\r
- sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ sortLabel.setFont(verdana11);\r
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
sortLabel.setText("Sort by ");\r
jPanel2.setBounds(new Rectangle(7, 17, 138, 242));\r
gridLayout2.setRows(8);\r
jPanel3.setBounds(new Rectangle(147, 46, 274, 26));\r
exportTab.setLayout(null);\r
- epsLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ epsLabel.setFont(verdana11);\r
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
epsLabel.setText("EPS Rendering Style");\r
- epsLabel.setBounds(new Rectangle(3, 47, 134, 21));\r
- epsRendering.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- epsRendering.setBounds(new Rectangle(145, 47, 286, 21));\r
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));\r
+ epsRendering.setFont(verdana11);\r
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
+ jLabel1.setFont(verdana11);\r
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
+ jLabel1.setText("/start-end suffix");\r
+ jLabel2.setFont(verdana11);\r
+ jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel2.setHorizontalTextPosition(SwingConstants.RIGHT);\r
+ jLabel2.setText("Database ref prefix");\r
+ jLabel1.setFont(verdana11);\r
+ jLabel2.setFont(verdana11);\r
+ fastajv.setFont(verdana11);\r
+ fastajv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ jLabel10.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ jLabel10.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel10.setText("(Uniprot|P02055)");\r
+ jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ jLabel11.setHorizontalAlignment(SwingConstants.CENTER);\r
+ jLabel11.setText("(/15-380)");\r
+ clustaldb.setFont(verdana11);\r
+ clustaldb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ clustaldb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ clustaldb.setText("Clustal ");\r
+ blcdb.setFont(verdana11);\r
+ blcdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ blcdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ blcdb.setText("BLC ");\r
+ fastadb.setFont(verdana11);\r
+ fastadb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ fastadb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ fastadb.setText("Fasta ");\r
+ msfdb.setFont(verdana11);\r
+ msfdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ msfdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ msfdb.setText("MSF ");\r
+ pfamdb.setFont(verdana11);\r
+ pfamdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ pfamdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ pfamdb.setText("PFAM ");\r
+ pileupdb.setFont(verdana11);\r
+ pileupdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ pileupdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ pileupdb.setText("Pileup ");\r
+ msfjv.setFont(verdana11);\r
+ msfjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ pirdb.setFont(verdana11);\r
+ pirdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ pirdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ pirdb.setText("PIR ");\r
+ jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jPanel11.setBorder(titledBorder2);\r
+ jPanel11.setBounds(new Rectangle(18, 72, 325, 182));\r
+ jPanel11.setLayout(gridLayout3);\r
+ gridLayout3.setColumns(2);\r
+ gridLayout3.setRows(9);\r
+ blcjv.setFont(verdana11);\r
+ blcjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ clustaljv.setFont(verdana11);\r
+ clustaljv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ pfamjv.setFont(verdana11);\r
+ pfamjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ pileupjv.setFont(verdana11);\r
+ pileupjv.setHorizontalAlignment(SwingConstants.CENTER);\r
+ pirjv.setFont(verdana11);\r
+ pirjv.setHorizontalAlignment(SwingConstants.CENTER);\r
jPanel2.add(fullScreen);\r
jPanel2.add(annotations);\r
jPanel2.add(fullID);\r
, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
new Insets(15, 0, 0, 15), 307, 1));\r
\r
- exportTab.add(epsLabel);\r
- exportTab.add(epsRendering);\r
\r
jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
, GridBagConstraints.WEST,\r
gapSymbolCB.setRenderer(dlcr);\r
\r
tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab, "Connections");\r
- tabbedPane.add(exportTab, "Export");\r
+ tabbedPane.add(connectTab,"Connections");\r
+ tabbedPane.add(exportTab, "File");\r
+ jPanel11.add(jLabel2);\r
+ jPanel11.add(jLabel1);\r
+ jPanel11.add(jLabel10);\r
+ jPanel11.add(jLabel11);\r
+ jPanel11.add(blcdb);\r
+ jPanel11.add(blcjv);\r
+ jPanel11.add(clustaldb);\r
+ jPanel11.add(clustaljv);\r
+ jPanel11.add(fastadb);\r
+ jPanel11.add(fastajv);\r
+ jPanel11.add(msfdb);\r
+ jPanel11.add(msfjv);\r
+ jPanel11.add(pfamdb);\r
+ jPanel11.add(pfamjv);\r
+ jPanel11.add(pileupdb);\r
+ jPanel11.add(pileupjv);\r
+ jPanel11.add(pirdb);\r
+ jPanel11.add(pirjv);\r
+ exportTab.add(epsLabel);\r
+ exportTab.add(epsRendering);\r
+ exportTab.add(jPanel11);\r
}\r
\r
/**\r
String key = (String) e.nextElement();\r
Vector tmp = (Vector) codonHash.get(key);\r
\r
- if (tmp.contains(codon))\r
+ if (tmp.contains(codon.toUpperCase()))\r
{\r
return key;\r
}\r
*/\r
public class Comparison\r
{\r
- /** DOCUMENT ME!! */\r
- public static String GapChars = " .-";\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ii DOCUMENT ME!\r
- * @param jj DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj)\r
+ /** DOCUMENT ME!! */\r
+ public static String GapChars = " .-";\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ii DOCUMENT ME!\r
+ * @param jj DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj)\r
+ {\r
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
+ }\r
+\r
+ /**\r
+ * this was supposed to be an ungapped pid calculation\r
+ * @param ii SequenceI\r
+ * @param jj SequenceI\r
+ * @param start int\r
+ * @param end int\r
+ * @return float\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
+ {\r
+ String si = ii.getSequence();\r
+ String sj = jj.getSequence();\r
+\r
+ int ilen = si.length() - 1;\r
+ int jlen = sj.length() - 1;\r
+\r
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
{\r
- return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
+ ilen--;\r
}\r
\r
- /**\r
- * this was supposed to be an ungapped pid calculation\r
- * @param ii SequenceI\r
- * @param jj SequenceI\r
- * @param start int\r
- * @param end int\r
- * @return float\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
{\r
- String si = ii.getSequence();\r
- String sj = jj.getSequence();\r
+ jlen--;\r
+ }\r
\r
- int ilen = si.length() - 1;\r
- int jlen = sj.length() - 1;\r
+ int count = 0;\r
+ int match = 0;\r
+ float pid = -1;\r
\r
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
- {\r
- ilen--;\r
- }\r
-\r
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
+ if (ilen > jlen)\r
+ {\r
+ for (int j = 0; j < jlen; j++)\r
+ {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1)))\r
{\r
- jlen--;\r
+ match++;\r
}\r
\r
- int count = 0;\r
- int match = 0;\r
- float pid = -1;\r
+ count++;\r
+ }\r
\r
- if (ilen > jlen)\r
- {\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) ilen * 100;\r
- }\r
- else\r
+ pid = (float) match / (float) ilen * 100;\r
+ }\r
+ else\r
+ {\r
+ for (int j = 0; j < jlen; j++)\r
+ {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1)))\r
{\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) jlen * 100;\r
+ match++;\r
}\r
\r
- return pid;\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) jlen * 100;\r
}\r
\r
- /**\r
- * this is a gapped PID calculation\r
- *\r
- * @param s1 SequenceI\r
- * @param s2 SequenceI\r
- * @return float\r
- */\r
- public static float PID(SequenceI s1, SequenceI s2)\r
+ return pid;\r
+ }\r
+\r
+ /**\r
+ * this is a gapped PID calculation\r
+ *\r
+ * @param s1 SequenceI\r
+ * @param s2 SequenceI\r
+ * @return float\r
+ */\r
+ public static float PID(SequenceI s1, SequenceI s2)\r
+ {\r
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length())\r
{\r
- int len;\r
+ len = s1.getSequence().length();\r
+ }\r
+ else\r
+ {\r
+ len = s2.getSequence().length();\r
+ }\r
\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
+ int bad = 0;\r
+\r
+ for (int i = 0; i < len; i++)\r
+ {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length())\r
+ {\r
+ chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length())\r
+ {\r
+ chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (! (jalview.util.Comparison.isGap(chr1)) &&\r
+ ! (jalview.util.Comparison.isGap(chr2)))\r
+ {\r
+ if (chr1 != chr2)\r
{\r
- len = s2.getSequence().length();\r
+ bad++;\r
}\r
+ }\r
+ }\r
\r
- int bad = 0;\r
+ return ( (float) 100 * (len - bad)) / len;\r
+ }\r
\r
- for (int i = 0; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (!(jalview.util.Comparison.isGap(chr1)) &&\r
- !(jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
- }\r
+ // Another pid with region specification\r
+ public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+ {\r
+ int len;\r
\r
- return ((float) 100 * (len - bad)) / len;\r
+ if (s1.getSequence().length() > s2.getSequence().length())\r
+ {\r
+ len = s1.getSequence().length();\r
+ }\r
+ else\r
+ {\r
+ len = s2.getSequence().length();\r
}\r
\r
- // Another pid with region specification\r
- public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+ if (end < len)\r
{\r
- int len;\r
+ len = end;\r
+ }\r
\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
+ if (len < start)\r
+ {\r
+ start = len - 1; // we just use a single residue for the difference\r
+ }\r
\r
- if (end < len)\r
- {\r
- len = end;\r
- }\r
+ int bad = 0;\r
\r
- if (len < start)\r
+ for (int i = start; i < len; i++)\r
+ {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length())\r
+ {\r
+ chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length())\r
+ {\r
+ chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (! (jalview.util.Comparison.isGap(chr1)) &&\r
+ ! (jalview.util.Comparison.isGap(chr2)))\r
+ {\r
+ if (chr1 != chr2)\r
{\r
- start = len - 1; // we just use a single residue for the difference\r
+ bad++;\r
}\r
+ }\r
+ }\r
\r
- int bad = 0;\r
-\r
- for (int i = start; i < len; i++)\r
+ return ( (float) 100 * (len - bad)) / len;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static boolean isGap(char c)\r
+ {\r
+ return (c == '-' || c == '.' || c == ' ') ? true : false;\r
+ }\r
+\r
+ public static boolean isNucleotide(SequenceI [] seqs)\r
+ {\r
+ int i = 0, iSize = seqs.length, j, jSize;\r
+ float nt = 0, aa = 0;\r
+ char c;\r
+ while (i < iSize)\r
+ {\r
+ jSize = seqs[i].getLength();\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ c = seqs[i].getCharAt(j);\r
+ if ('a' <= c && c <= 'z')\r
+ c -= ('a' - 'A');\r
+\r
+ if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')\r
+ nt++;\r
+ else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j)))\r
{\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (!(jalview.util.Comparison.isGap(chr1)) &&\r
- !(jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
+ aa++;\r
}\r
-\r
- return ((float) 100 * (len - bad)) / len;\r
+ }\r
+ i++;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static boolean isGap(char c)\r
- {\r
- return ( c=='-' || c=='.' || c==' ' ) ? true : false;\r
- }\r
+ if ( (nt / (nt + aa)) > 0.85f)\r
+ return true;\r
+ else\r
+ return false;\r
+\r
+ }\r
}\r
msf[0].getSequence()));\r
\r
this.msa = new vamsas.objects.simple.Msfalignment();\r
- msa.setMsf(jalview.io.PileUpfile.print(msf));\r
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
+ msa.setMsf(pileup.print(msf));\r
}\r
\r
public void run()\r
return false;\r
}\r
\r
- Object other = (Object) obj;\r
+ //Object other = (Object) obj;\r
\r
if (obj == null) {\r
return false;\r
git://source.jalview.org / jalview.git / commitdiff