Author: chinmoy
Date: 2009-08-06 23:21:26 -0700 (Thu, 06 Aug 2009)
New Revision: 17734
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/PhylotreePlugin.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/ui/PhyloFileDialog.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
Log:
Added file validation for phylip files
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/PhylotreePlugin.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/PhylotreePlugin.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/PhylotreePlugin.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -43,22 +43,6 @@
//(2) add another menu item: Layout->Phylotree layouts
-
-// RectangularCladogram a = new RectangularCladogram();
-// CyLayouts.addLayout(a,"Phylotree Layouts");
-//
-//
Cytoscape.getDesktop().update(Cytoscape.getDesktop().getGraphics());
-//
-// JMenu j = Cytoscape.getDesktop().getCyMenus().getLayoutMenu();
-// JMenuItem jt;
-//
-// for(int i = 0; i<j.getItemCount(); i++)
-// {
-// jt= j.getItem(i);
-// if(jt!=null)
-// System.out.println("Name: "+i+" "+jt.getText());
-// }
-
PhyloTreeLayoutAction layoutAction = new
PhyloTreeLayoutAction(new RectangularCladogram());
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
layoutAction);
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -24,19 +24,23 @@
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.cytoscape.phylotree.visualstyle.DepthwiseColor;
-import org.cytoscape.phylotree.visualstyle.PhyloVisualStyle;
+import org.cytoscape.phylotree.visualstyle.DepthwiseSize;
import org.cytoscape.phylotree.visualstyle.PhyloVisualStyleManager;
+import java.io.BufferedReader;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
import java.io.IOException;
import java.util.List;
import java.util.Iterator;
+import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.CyLayouts;
public class PhyloTreeImportAction extends CytoscapeAction{
-
+
public PhyloTreeImportAction(PhylotreePlugin p) {
// Add the menu item under menu pulldown "File->Import"
super("Phylogenetic tree...");
@@ -53,43 +57,46 @@
System.out.println("pFile = null");
return;
}
-
+
if (pFormat.equalsIgnoreCase("phylip")){
- loadnetwork_phylip(pFile);
+ if(validatePhylipFile(pFile))
+ loadnetwork_phylip(pFile);
}
else if (pFormat.equalsIgnoreCase("phyloxml")){
loadnetwork_phyloXML(pFile);
}
-
+
// Add the phylogenetic tree specific visual styles
PhyloVisualStyleManager phyloVSMan = new
PhyloVisualStyleManager();
+ phyloVSMan.addVisualStyle(new DepthwiseSize());
phyloVSMan.addVisualStyle(new DepthwiseColor());
-
+
+
}
-
-
+
+
private void loadnetwork_phylip(File pFile) {
// Use the parser to read the file
-
+
// Parse the file
PhylipTreeImpl phylipParser = new PhylipTreeImpl(pFile);
-
+
CyNetwork cyNetwork = Cytoscape.createNetwork(pFile.getName(),
true);
-
+
CyAttributes cyAttributes = Cytoscape.getEdgeAttributes();
-
-
+
+
// Get all nodes in the PHYLIP tree
List<PhylotreeNode> nodeList = phylipParser.getNodeList();
-
+
// For each node, get all edges
for(Iterator<PhylotreeNode> nodeListIterator =
nodeList.iterator(); nodeListIterator.hasNext();)
{
PhylotreeNode pNode = nodeListIterator.next();
-
+
// Get edges
List<PhylotreeEdge> edgeList =
phylipParser.getEdges(pNode);
-
+
// For each edge, create the two nodes connected if
they do not exist
for(Iterator<PhylotreeEdge> edgeListIterator =
edgeList.iterator(); edgeListIterator.hasNext();)
{
@@ -97,9 +104,9 @@
CyNode node1 =
Cytoscape.getCyNode(pEdge.getSourceNode().getName(), true);
CyNode node2 =
Cytoscape.getCyNode(pEdge.getTargetNode().getName(), true);
-
+
CyEdge cyEdge = Cytoscape.getCyEdge(node1,
node2, Semantics.INTERACTION, "pp", true, true);
-
+
// Get edge attributes and set them
List<Object> edgeAttributes =
phylipParser.getEdgeAttribute(pEdge);
cyAttributes.setAttribute(cyEdge.getIdentifier(), "branchLength",
(Double)edgeAttributes.get(0));
@@ -108,34 +115,38 @@
cyNetwork.addNode(node2);
}
}
-
+
cyAttributes.setUserEditable("branchLength", false);
cyAttributes.setUserVisible("branchLength", true);
// Apply default layout
CyLayouts.getLayout("slanted_cladogram").doLayout();
-
+
+
// Apply visual style
Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null,
"phyloVizMap.props");
}
-
+
private void loadnetwork_phyloXML(File pFile) {
-// PhyloXmlParser parser = new PhyloXmlParser();
+
+ // PhyloXmlParser parser = new PhyloXmlParser();
PhylogenyParser parser = new PhyloXmlParser();
- //parser.setSource(pFile);
+
PhylogenyFactory factory =
ParserBasedPhylogenyFactory.getInstance();
Phylogeny[] trees;
try {
trees = factory.create(pFile, parser);
- //trees = parser.parse();
-
+
+
}
catch (PhylogenyParserException ppe){
System.out.println("PhloXML Parser error occured.");
+ System.out.println("Verify that file is a valid
PhyloXML file.");
+
return;
}
catch(IOException ioe){
@@ -145,82 +156,127 @@
for (int i=0; i< trees.length; i++){
PhylogenyNodeIterator it =
trees[i].iteratorLevelOrder();
-
-
-
+
+
+
// Create a network
CyNetwork cyNetwork =
Cytoscape.createNetwork(trees[i].getName(), true);
-
-
-
+
+
+
// Add network attributes
addPhyloXMLNetworkAttributes(trees[i],
cyNetwork.getIdentifier());
-
+
int unnamedNodeIndex = 0;
// process each node, get node, edge and attributes
while (it.hasNext())
{
PhylogenyNode node = (PhylogenyNode) it.next();
PhylogenyNode parent = node.getParent(); // for
edge
-
-
+
+
// Add the node to the network
if(node.getNodeName().equals(""))
- {
+ {
node.setName("Node"+unnamedNodeIndex);
unnamedNodeIndex++;
- }
+ }
CyNode cyNode =
Cytoscape.getCyNode(node.getNodeName(), true);
// Add the node's attributes
-
+
cyNetwork.addNode(cyNode);
-
+
addPhyloXMLNodeAttributes(node,
cyNode.getIdentifier());
-
+
// If parent exists, add it as well as all
edges connecting the two
if(parent!=null)
{
CyNode cyParent =
Cytoscape.getCyNode(parent.getNodeName(), true);
-
+
if(cyParent.getRootGraphIndex()!=cyNode.getRootGraphIndex())
{
- // Add the parent's attributes
- CyEdge cyEdge =
Cytoscape.getCyEdge(cyParent, cyNode, Semantics.INTERACTION, "pp", true, true);
- // Add the edge's attributes
+ // Add the parent's attributes
+ CyEdge cyEdge =
Cytoscape.getCyEdge(cyParent, cyNode, Semantics.INTERACTION, "pp", true, true);
+ // Add the edge's attributes
- cyNetwork.addEdge(cyEdge);
- addPhyloXMLEdgeAttributes(node,
cyEdge.getIdentifier());
-
+ cyNetwork.addEdge(cyEdge);
+ addPhyloXMLEdgeAttributes(node,
cyEdge.getIdentifier());
+
}
}
}
-
-
+
+
// Apply default layout
CyLayouts.getLayout("slanted_cladogram").doLayout();
-
+
// Apply visual style
Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED,
null, "phyloVizMap.props");
}
-
+
}
-
+
+ private boolean validatePhylipFile(File file)
+ {
+ // Read the file to obtain the tree
+ if(file!=null)
+ {
+ PhylipTreeImpl phylipParser = new PhylipTreeImpl(file);
+
+
+ String fileStr = phylipParser.getTreeTextFromFile(file);
+
+
+ // Check to make sure file is a complete tree
+ int numOpenParens = 0;
+ int numCloseParens = 0;
+
+ for(int i = 0; i<fileStr.length(); i++)
+ {
+ if(fileStr.charAt(i)=='(')
+ numOpenParens++;
+ else if(fileStr.charAt(i)==')')
+ numCloseParens++;
+ }
+
+ if(numOpenParens!=numCloseParens)
+ {
+ System.out.println("File is not a valid
Phylip/Newick format file.");
+ System.out.println("Number of '(' not equal to
')'.");
+ return false;
+ }
+
+
+ // Check to make sure file is not an empty tree
+ if(numOpenParens==0)
+ {
+ System.out.println("File is not a valid
Phylip/Newick format file.");
+ System.out.println("Tree in the file does not
consist of any nodes.");
+ return false;
+ }
+
+ return true;
+ }
+ else
+ return false;
+ }
+
private void addPhyloXMLNetworkAttributes(Phylogeny phy, String
networkID )
{
CyAttributes networkAttributes =
Cytoscape.getNetworkAttributes();
-
+
// Check and assign network attributes
if(!phy.getName().equals(""))
networkAttributes.setAttribute(networkID,"Name",phy.getName());
-
+
if(phy.getIdentifier()!=null)
networkAttributes.setAttribute(networkID, "ID",
phy.getIdentifier().getValue());
if(!phy.getDescription().equals(""))
networkAttributes.setAttribute(networkID,"Description",phy.getDescription());
-
+
if(phy.getConfidence()!=null)
networkAttributes.setAttribute(networkID,"Confidence",phy.getConfidence().getValue());
if(phy.isRooted())
@@ -231,26 +287,26 @@
networkAttributes.setAttribute(networkID, "Rerootable",
true);
else
networkAttributes.setAttribute(networkID, "Rerootable",
false);
-
+
if(!phy.getType().equals(""))
networkAttributes.setAttribute(networkID,"Type",phy.getType());
-
+
if(!phy.getDistanceUnit().equals(""))
networkAttributes.setAttribute(networkID,"Distance
Unit",phy.getDistanceUnit());
-
+
Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED,
null, null);
-
+
}
private void addPhyloXMLNodeAttributes(PhylogenyNode node, String
nodeID )
{
NodeData nodeData = node.getNodeData();
-
+
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
-
+
// Check and assign node attributes
-
+
if(nodeData.isHasTaxonomy())
{
if(!nodeData.getTaxonomy().getCommonName().equals(""))
@@ -275,14 +331,14 @@
nodeAttributes.setAttribute(nodeID,
"Taxonomy: URI Description", nodeData.getTaxonomy().getUri().getDescription());
}
}
-
+
if(nodeData.isHasBinaryCharacters())
{
- nodeAttributes.setAttribute(nodeID, "Binary
Characters", nodeData.getBinaryCharacters().toString());
+ nodeAttributes.setAttribute(nodeID, "Binary
Characters", nodeData.getBinaryCharacters().toString());
}
-
-
-
+
+
+
if(nodeData.isHasDate())
{
if(nodeData.getDate().getRange()!=null)
@@ -293,10 +349,10 @@
nodeAttributes.setAttribute(nodeID, "Date:
Description", nodeData.getDate().getDesc());
if(nodeData.getDate().getValue()!=null)
nodeAttributes.setAttribute(nodeID, "Date:
Value", nodeData.getDate().getValue().toString());
-
-
+
+
}
-
+
if(nodeData.isHasDistribution())
{
if(nodeData.getDistribution().getAltitude()!=null)
@@ -309,30 +365,30 @@
nodeAttributes.setAttribute(nodeID,
"Distribution: Latitude", nodeData.getDistribution().getLatitude().toString());
if(nodeData.getDistribution().getLongitude()!=null)
nodeAttributes.setAttribute(nodeID,
"Distribution: Longitude",
nodeData.getDistribution().getLongitude().toString());
-
+
}
-
+
if(nodeData.isHasEvent())
{
if(nodeData.getEvent().getEventType()!=null)
nodeAttributes.setAttribute(nodeID, "Event:
Type", nodeData.getEvent().getEventType().name());
if(nodeData.getEvent().getConfidence()!=null)
nodeAttributes.setAttribute(nodeID, "Event:
Confidence", nodeData.getEvent().getConfidence().getType());
-
+
nodeAttributes.setAttribute(nodeID, "Event: #
Duplications", nodeData.getEvent().getNumberOfDuplications());
nodeAttributes.setAttribute(nodeID, "Event: # Gene
Losses", nodeData.getEvent().getNumberOfGeneLosses());
nodeAttributes.setAttribute(nodeID, "Event: #
Speciations", nodeData.getEvent().getNumberOfSpeciations());
-
+
}
-
+
if(nodeData.isHasNodeIdentifier())
{
-
+
if(!nodeData.getNodeIdentifier().getValue().equals(""))
nodeAttributes.setAttribute(nodeID,"Identifier",nodeData.getNodeIdentifier().getValue());
-
+
}
-
+
if(nodeData.isHasProperties())
{
Property[] props =
nodeData.getProperties().getPropertiesArray();
@@ -350,11 +406,11 @@
nodeAttributes.setAttribute(nodeID,"Property"+i+": Unit", props[i].getUnit());
if(!props[i].getValue().equals(""))
nodeAttributes.setAttribute(nodeID,"Property"+i+": Value", props[i].getValue());
-
+
}
-
+
}
-
+
if(nodeData.isHasReference())
{
if(!nodeData.getReference().getDoi().equals(""))
@@ -362,7 +418,7 @@
if(!nodeData.getReference().getValue().equals(""))
nodeAttributes.setAttribute(nodeID,"Reference:
Value", nodeData.getReference().getValue());
}
-
+
if(nodeData.isHasSequence())
{
@@ -374,13 +430,13 @@
if(nodeData.getSequence().getName().equals(""))
nodeAttributes.setAttribute(nodeID, "Sequence:
Name", nodeData.getSequence().getName());
-
+
if(nodeData.getSequence().getSymbol().equals(""))
nodeAttributes.setAttribute(nodeID, "Sequence:
Symbol", nodeData.getSequence().getSymbol());
-
+
if(nodeData.getSequence().getType().equals(""))
nodeAttributes.setAttribute(nodeID, "Sequence:
Type", nodeData.getSequence().getType());
-
+
if(nodeData.getSequence().getUri()!=null)
{
if(!nodeData.getSequence().getUri().getValue().toString().equals(""))
@@ -390,16 +446,16 @@
if(!nodeData.getSequence().getUri().getDescription().equals(""))
nodeAttributes.setAttribute(nodeID,
"Sequence: URI Description", nodeData.getSequence().getUri().getDescription());
}
-
+
if(nodeData.getSequence().getAccession()!=null)
{
if(!nodeData.getSequence().getAccession().getSource().equals(""))
nodeAttributes.setAttribute(nodeID,
"Sequence: Accession Source",
nodeData.getSequence().getAccession().getSource());
if(!nodeData.getSequence().getAccession().getValue().equals(""))
nodeAttributes.setAttribute(nodeID,
"Sequence: Accession", nodeData.getSequence().getAccession().getValue());
-
+
}
-
+
if(nodeData.getSequence().getDomainArchitecture()!=null)
{
nodeAttributes.setAttribute(nodeID, "Sequence:
Domain Total Length",
nodeData.getSequence().getDomainArchitecture().getTotalLength());
@@ -407,22 +463,22 @@
{
if(!nodeData.getSequence().getDomainArchitecture().getDomain(i).getId().equals(""))
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" ID",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getId());
-
+
if(!nodeData.getSequence().getDomainArchitecture().getDomain(i).getName().equals(""))
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" Name",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getName());
-
-
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" Confidence",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getConfidence());
-
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" From",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getFrom());
-
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" To",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getTo());
-
nodeAttributes.setAttribute(nodeID, "Sequence: Domain"+i+" Length",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getLength());
-
+
+ nodeAttributes.setAttribute(nodeID,
"Sequence: Domain"+i+" Confidence",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getConfidence());
+ nodeAttributes.setAttribute(nodeID,
"Sequence: Domain"+i+" From",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getFrom());
+ nodeAttributes.setAttribute(nodeID,
"Sequence: Domain"+i+" To",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getTo());
+ nodeAttributes.setAttribute(nodeID,
"Sequence: Domain"+i+" Length",
nodeData.getSequence().getDomainArchitecture().getDomain(i).getLength());
+
}
-
+
}
-
+
List<PhylogenyData> annotations =
nodeData.getSequence().getAnnotations();
Iterator<PhylogenyData> iterator =
annotations.iterator();
-
+
int index = 0;
while(iterator.hasNext())
{
@@ -431,16 +487,16 @@
nodeAttributes.setAttribute(nodeID,
"Sequence: Annotation"+index, data.toString());
index++;
}
-
-
-
-
+
+
+
+
}
-
+
Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED,
null, null);
}
-
-
+
+
private void addPhyloXMLEdgeAttributes(PhylogenyNode node, String
edgeID )
{
BranchData branchData = node.getBranchData();
@@ -453,7 +509,7 @@
if(branchData.getBranchColor()!=null)
edgeAttributes.setAttribute(edgeID, "Color",
branchData.getBranchColor().getValue().toString());
-
+
List<Confidence> confidences = branchData.getConfidences();
Iterator<Confidence> iterator = confidences.iterator();
int index = 0;
@@ -463,10 +519,10 @@
edgeAttributes.setAttribute(edgeID, "Confidence"+index,
c.getValue());
edgeAttributes.setAttribute(edgeID,
"Confidence"+index+" type", c.getType());
index++;
-
+
}
-
+
}
-
-
+
+
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -95,12 +95,17 @@
return "Circular Cladogram Layout";
}
-
+ public void construct(double radius)
+ {
+ BASE_RADIUS += radius;
+ construct();
+ }
+
public void construct() {
taskMonitor.setStatus("Initializing");
initialize();
+
-
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -94,8 +94,13 @@
public String toString(){
return "Radial Cladogram Layout";
}
+
+ public void construct(double radius)
+ {
+ BASE_RADIUS = radius;
+ construct();
+ }
-
public void construct() {
taskMonitor.setStatus("Initializing");
initialize();
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -94,7 +94,11 @@
public String toString(){
return "Rectangular Cladogram Layout";
}
-
+ public void construct(double distance)
+ {
+ INTERNODE_DISTANCE += distance;
+ construct();
+ }
public void construct() {
taskMonitor.setStatus("Initializing");
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -95,8 +95,12 @@
public String toString(){
return "Slanted Cladogram Layout";
}
+ public void construct(double distance)
+ {
+ INTERNODE_DISTANCE += distance;
+ construct();
+ }
-
public void construct() {
taskMonitor.setStatus("Initializing");
initialize();
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -43,7 +43,7 @@
/*
* Reads a PHYLIP file and returns the tree in string format
*/
- private String getTreeTextFromFile(File pTreeFile){
+ public String getTreeTextFromFile(File pTreeFile){
String retStr = null;
try
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/ui/PhyloFileDialog.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/ui/PhyloFileDialog.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/ui/PhyloFileDialog.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -2,6 +2,8 @@
import javax.swing.JDialog;
import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileFilter;
+
import cytoscape.Cytoscape;
import java.io.File;
import org.cytoscape.phylotree.actions.PhyloTreeImportAction;
@@ -138,13 +140,16 @@
private void btnFileActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser chooser = new JFileChooser(System.getProperty("user.dir"));
chooser.setAcceptAllFileFilterUsed(false);
- //chooser.addChoosableFileFilter(new TxtFileFilter());
+
+ chooser.addChoosableFileFilter(new PhylipFileFilter());
+ chooser.addChoosableFileFilter(new PhyloXMLFileFilter());
int returnVal = chooser.showOpenDialog(this);
if(returnVal == JFileChooser.APPROVE_OPTION) {
selectedFile = chooser.getSelectedFile();
+ tfFileName.setText(selectedFile.getName());
}
- tfFileName.setText(selectedFile.getName());
+
}
private void btnCancelActionPerformed(java.awt.event.ActionEvent evt) {
@@ -178,4 +183,76 @@
private javax.swing.JTextField tfFileName;
// End of variables declaration
+
+ // Inner classes - file filters for Phylip and phyloxml format
+ class PhylipFileFilter extends FileFilter{
+ //Accept all directories and all gif, jpg, tiff, or png files.
+ public boolean accept(File f) {
+ if (f.isDirectory()) {
+ return true;
+ }
+
+ String extension = getExtension(f);
+ if (extension != null) {
+ if (extension.equals("nh") || extension.equals("newick") ||
extension.equals("phy"))
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ //The description of this filter
+ public String getDescription() {
+ return "Newick and Phylip format files";
+ }
+
+ }
+
+ class PhyloXMLFileFilter extends FileFilter{
+ public boolean accept(File f) {
+ if (f.isDirectory()) {
+ return true;
+ }
+
+ String extension = getExtension(f);
+ if (extension != null) {
+ if (extension.equals("phyloxml") || extension.equals("xml"))
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ //The description of this filter
+ public String getDescription() {
+ return "PhyloXML format files";
+ }
+
+ }
+
+ /*
+ * Get the extension of a file.
+ */
+ public String getExtension(File f) {
+ String ext = null;
+ String s = f.getName();
+ int i = s.lastIndexOf('.');
+
+ if (i > 0 && i < s.length() - 1) {
+ ext = s.substring(i+1).toLowerCase();
+ }
+ return ext;
+ }
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
2009-08-07 06:18:07 UTC (rev 17733)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
2009-08-07 06:21:26 UTC (rev 17734)
@@ -5,8 +5,6 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
-import cytoscape.visual.Appearance;
-import cytoscape.visual.ArrowShape;
import cytoscape.visual.EdgeAppearance;
import cytoscape.visual.EdgeAppearanceCalculator;
import cytoscape.visual.GlobalAppearanceCalculator;
@@ -19,7 +17,6 @@
import cytoscape.visual.calculators.Calculator;
import cytoscape.visual.mappings.BoundaryRangeValues;
import cytoscape.visual.mappings.ContinuousMapping;
-import cytoscape.visual.mappings.DiscreteMapping;
import cytoscape.visual.mappings.Interpolator;
import cytoscape.visual.mappings.LinearNumberToColorInterpolator;
import cytoscape.visual.mappings.ObjectMapping;
@@ -35,6 +32,8 @@
public class DepthwiseSize implements PhyloVisualStyle {
+
+ static double MAX_SIZE = 135.0;
public String getName()
{
@@ -68,21 +67,19 @@
nodeApp.set(VisualPropertyType.NODE_LABEL_POSITION, new
LabelPosition(5,3,2,0,0));
nodeApp.set(VisualPropertyType.NODE_FONT_SIZE,20);
-
nodeAppCalc.setDefaultAppearance(nodeApp);
// Add edge appearance specific settings
EdgeAppearance edgeApp = new EdgeAppearance();
edgeApp.set(VisualPropertyType.EDGE_LABEL_COLOR, Color.WHITE);
edgeApp.set(VisualPropertyType.EDGE_FONT_SIZE,20);
- edgeApp.set(VisualPropertyType.EDGE_LINE_WIDTH,10);
+ edgeApp.set(VisualPropertyType.EDGE_LINE_WIDTH,5);
edgeAppCalc.setDefaultAppearance(edgeApp);
-
nodeAppCalc.setCalculator(createNodeColorCalculator(network));
nodeAppCalc.setCalculator(createNodeSizeCalculator(network));
edgeAppCalc.setCalculator(createEdgeColorCalculator(network));
-
+
// Create the visual style
VisualStyle visualStyle = new VisualStyle("DepthwiseSize",
nodeAppCalc, edgeAppCalc, globalAppCalc);
@@ -300,7 +297,7 @@
// Set controlling Attribute
cm.setControllingAttributeName("Depth",
Cytoscape.getCurrentNetwork(), false);
- Double underSize = 135.0;
+ Double underSize = MAX_SIZE;
Double minSize = 110.0;
Double midSize = 85.0;
Double maxSize = 60.0;
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