Author: scooter
Date: 2010-11-22 22:29:33 -0800 (Mon, 22 Nov 2010)
New Revision: 22992
Added:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
Log:
Put resources in the right place and support List arguments
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2010-11-23 06:28:44 UTC (rev 22991)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2010-11-23 06:29:33 UTC (rev 22992)
@@ -76,6 +76,7 @@
public static final String CLEAR = "clear";
public static final String CURRENT = "current";
public static final String LABELS = "labellist";
+ public static final String LIST = "list";
public static final String NETWORK = "network";
public static final String NODE = "node";
public static final String NODELIST = "nodelist";
@@ -99,6 +100,9 @@
addDescription(CLEAR, "Remove all charts from a node");
addArgument(CLEAR, NODE);
addArgument(CLEAR, NODELIST, SELECTED);
+
+ addDescription(LIST, "List available chart types");
+ addArgument(LIST);
}
public CyCommandResult execute(String command, Collection<Tunable>args)
@@ -119,6 +123,15 @@
throws
CyCommandException, RuntimeException {
CyCommandResult result = new CyCommandResult();
+ if (command.equals(LIST)) {
+ result.addMessage("Available chart types: ");
+ for (String type: viewerMap.keySet()) {
+ result.addMessage(" "+type);
+ }
+ result.addResult("typeList", new
ArrayList<String>(viewerMap.keySet()));
+ return result;
+ }
+
if (!args.containsKey(NODE) && !args.containsKey(NODELIST)) {
throw new CyCommandException("node or nodelist to map
chart to must be specified");
}
@@ -165,13 +178,13 @@
List<Double> values = null;
if (args.containsKey(VALUES)) {
// Get our values. convertData returns an array of
values in degrees of arc
- values =
ValueUtils.convertInputToDouble((String)args.get(VALUES));
+ values =
ValueUtils.convertInputToDouble(args.get(VALUES));
}
List<String> labels = new ArrayList<String>();
if (args.containsKey(LABELS)) {
// Get our labels. These may or may not be printed
depending on options
- labels =
ValueUtils.getStringList((String)args.get(LABELS));
+ labels = ValueUtils.getStringList(args.get(LABELS));
}
// Get our position
@@ -188,7 +201,7 @@
// If we've got an attributelist, we need to get our
values now since they will change based on
// the node
if (args.containsKey(ATTRIBUTELIST))
- values = ValueUtils.getDataFromAttributes
(node, (String)args.get(ATTRIBUTELIST), labels);
+ values = ValueUtils.getDataFromAttributes
(node, args.get(ATTRIBUTELIST), labels);
List<CustomGraphic> cgList =
viewer.getCustomGraphics(args, values, labels, node, view, pos);
ViewUtils.addCustomGraphics(cgList, node, view);
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2010-11-23 06:28:44 UTC (rev 22991)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2010-11-23 06:29:33 UTC (rev 22992)
@@ -82,14 +82,22 @@
* @return the list of values
* @throws CyCommandException if the attributes aren't numeric
*/
- public static List<Double> getDataFromAttributes (CyNode node, String
attributesList, List<String> labels)
+ public static List<Double> getDataFromAttributes (CyNode node, Object
attributesList, List<String> labels)
throws CyCommandException {
if (attributesList == null)
throw new CyCommandException("no attributes with
data?");
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
String nodeName = node.getIdentifier();
- String[] attributeArray = attributesList.split(",");
+ String[] attributeArray = null;
+ if (attributesList instanceof String) {
+ attributeArray = ((String)attributesList).split(",");
+ } else if (attributesList instanceof List) {
+ String[] s = new String[1];
+ attributeArray =
((List<String>)attributesList).toArray(s);
+ } else {
+ return new ArrayList<Double>();
+ }
if (attributeArray.length == 1) {
// Handle the case where we were given a single, list
attribute
if (labels.size() == 0) {
@@ -163,14 +171,23 @@
public static List<Double> parseStringList(String input) throws
CyCommandException {
if (input == null)
throw new CyCommandException("no input data?");
-
- String[] inputArray = input.split(",");
+ String[] inputArray = ((String)input).split(",");
return convertStringList(Arrays.asList(inputArray));
}
- public static List<String> getStringList(String input) {
- String[] inputArray = input.split(",");
- return Arrays.asList(inputArray);
+ public static List<String> getStringList(Object input) {
+ if (input instanceof String) {
+ String[] inputArray = ((String)input).split(",");
+ return Arrays.asList(inputArray);
+ } else if (input instanceof List) {
+ List<String> result = new ArrayList<String>();
+ for (Object o: (List)input) {
+ result.add(o.toString());
+ }
+ return result;
+ }
+
+ return new ArrayList<String>();
}
/**
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
2010-11-23 06:28:44 UTC (rev 22991)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
2010-11-23 06:29:33 UTC (rev 22992)
@@ -219,7 +219,7 @@
// We don't want to scale down too far. If scale < 20%
of the font size, skip the label
if (scale < 0.20)
return null;
- System.out.println("scale = "+scale);
+ // System.out.println("scale = "+scale);
AffineTransform sTransform = new AffineTransform();
sTransform.scale(scale, scale);
lShape = sTransform.createTransformedShape(lShape);
Added:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
(rev 0)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
2010-11-23 06:29:33 UTC (rev 22992)
@@ -0,0 +1,27 @@
+# This props file would be filled out and included in the plugin jar file.
This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=nodeCharts
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Paint a chart on a node
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.9
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Visualization
+
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntstiutions=John "Scooter" Morris:UCSF;Allan
Kuchinsky:Agilent;Alex Pico:Gladtone Institutes
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
