Author: kono
Date: 2010-01-29 11:53:58 -0800 (Fri, 29 Jan 2010)
New Revision: 19071
Modified:
cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java
cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
cytoscape/trunk/src/cytoscape/data/readers/KeyValue.java
cytoscape/trunk/src/cytoscape/visual/AppearanceCalculator.java
Log:
Fixed NPE bug when loading GML file.
Modified: cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
2010-01-29 19:25:15 UTC (rev 19070)
+++ cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
2010-01-29 19:53:58 UTC (rev 19071)
@@ -40,16 +40,15 @@
import java.io.File;
import java.io.IOException;
-import java.util.regex.Pattern;
+import java.util.Set;
import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.CyLayouts;
import cytoscape.task.TaskMonitor;
import cytoscape.util.CyNetworkNaming;
import cytoscape.view.CyNetworkView;
-import cytoscape.Cytoscape;
-import java.util.Set;
/**
Modified: cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java 2010-01-29
19:25:15 UTC (rev 19070)
+++ cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java 2010-01-29
19:53:58 UTC (rev 19071)
@@ -33,77 +33,64 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
package cytoscape.data.readers;
-import cytoscape.util.FileUtil;
-import cytoscape.logger.CyLogger;
-
-import java.io.FileReader;
import java.io.FilterReader;
import java.io.IOException;
-import java.io.InputStreamReader;
import java.io.InputStream;
+import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StreamTokenizer;
import java.io.Writer;
-
import java.text.ParseException;
-
-import java.util.Iterator;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
-import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import cytoscape.util.FileUtil;
/**
- * The purpose of hte class is to translate gml into an object tree, and print
out an object treee
- * into GML
+ * The purpose of this class is to translate GML into an object tree, and print
+ * out an object tree into GML
*/
public class GMLParser {
/**
* This character begsin and ends a string literal in a GML file
*/
- static int QUOTE_CHAR = '"';
+ private static final int QUOTE_CHAR = '"';
/**
* String versio of above
*/
- static String QUOTE_STRING = "\"";
+ private static final String QUOTE_STRING = "\"";
/**
* This regex pattern will match a valid key
*/
- static Pattern keyPattern = Pattern.compile("\\w+");
- ;
+ private static final Pattern keyPattern = Pattern.compile("\\w+");;
/**
* This regex pattern will match a valid integer
*/
- static Pattern integerPattern = Pattern.compile("(\\+|\\-){0,1}\\d+");
- ;
+ private static final Pattern integerPattern =
Pattern.compile("(\\+|\\-){0,1}\\d+");;
/**
* This regex pattern will match a valid real (double)
*/
- static Pattern realPattern =
Pattern.compile("(\\+|\\-){0,1}\\d+\\.\\d+((E|e)(\\+|\\-){0,1}\\d+){0,1}");
- ;
+ private static final Pattern realPattern = Pattern
+
.compile("(\\+|\\-){0,1}\\d+\\.\\d+((E|e)(\\+|\\-){0,1}\\d+){0,1}");;
- /*
- * This string opens a list
- */
- static String LIST_OPEN = "[";
+ // opens a list
+ private static final String LIST_OPEN = "[";
- /**
- * This string close a list
- */
- static String LIST_CLOSE = "]";
- StreamTokenizer tokenizer;
+ // close a list
+ private static final String LIST_CLOSE = "]";
+
+ private StreamTokenizer tokenizer;
/**
- * Constructor has to initialize the relevenat
- * regular expression patterns
+ * Constructor has to initialize the relevenat regular expression
patterns
*/
public GMLParser(StreamTokenizer tokenizer) {
this.tokenizer = tokenizer;
@@ -112,15 +99,16 @@
/**
* Make a stream tokenizer out of the given this file and read in the
file
*/
- public GMLParser(String file) throws IOException, Exception {
+ public GMLParser(final String file) throws IOException, Exception {
this(FileUtil.getInputStream(file));
}
/**
* Make a stream tokenizer out of the given this file and read in the
file
*/
- public GMLParser(InputStream stream) throws IOException, Exception {
- tokenizer = new StreamTokenizer(new FilterNewlineReader(new
InputStreamReader(stream)));
+ public GMLParser(final InputStream stream) throws IOException,
Exception {
+ tokenizer = new StreamTokenizer(new FilterNewlineReader(
+ new InputStreamReader(stream)));
tokenizer.resetSyntax();
tokenizer.commentChar('#');
@@ -136,36 +124,36 @@
tokenizer.nextToken();
}
+
/**
- * Public method to print out a given object tree(list)
- * using the supplied filewriter
+ * Public method to print out a given object tree(list) using the
supplied
+ * filewriter
*/
- public static void printList(List list, Writer writer) throws
IOException {
+ public static void printList(final List<KeyValue> list, final Writer
writer) throws IOException {
printList(list, "", writer);
}
+
/**
* Protected recurive helper method to print out an object tree
*/
- protected static void printList(List list, String indent, Writer writer)
- throws IOException {
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.value instanceof List) {
- // If the value is a list, print that list
recursively
- // surrounded by the list open and close
characters
+ protected static void printList(final List<KeyValue> list, final String
indent, final Writer writer)
+ throws IOException {
+ for (KeyValue keyVal: list) {
+ if (keyVal.value instanceof List<?>) {
+ // If the value is a list, print that list
recursively
+ // surrounded by the list open and close
characters
writer.write(indent + keyVal.key + "\t");
writer.write(LIST_OPEN + "\n");
- printList((List) keyVal.value, indent + "\t",
writer);
+ printList((List<KeyValue>) keyVal.value, indent
+ "\t", writer);
writer.write(indent + LIST_CLOSE + "\n");
} else if (keyVal.value instanceof String) {
- // Surround a string with the quote characters
+ // Surround a string with the quote characters
writer.write(indent + keyVal.key + "\t");
writer.write(QUOTE_STRING + keyVal.value +
QUOTE_STRING + "\n");
} else if (keyVal.value instanceof Double) {
- // If the double contains a non-number, we
will refuse to write
- // it out because the result will be invalid
gml
+ // If the double contains a non-number, we will
refuse to write
+ // it out because the result will be invalid gml
Double value = (Double) keyVal.value;
if (!(value.isNaN() || value.isInfinite())) {
@@ -173,8 +161,8 @@
writer.write(keyVal.value + "\n");
}
} else if (keyVal.value instanceof Integer) {
- // Everything else (Integer, double) relies
upon the default
- // toString() method of the object
+ // Everything else (Integer, double) relies
upon the default
+ // toString() method of the object
writer.write(indent + keyVal.key + "\t");
writer.write(keyVal.value + "\n");
}
@@ -184,8 +172,8 @@
/**
* A list consists of zero or more paris of keys and values
*/
- public Vector parseList() throws IOException, ParseException {
- Vector result = new Vector();
+ public List<KeyValue> parseList() throws IOException, ParseException {
+ final List<KeyValue> result = new ArrayList<KeyValue>();
while (isKey()) {
String key = parseKey();
@@ -199,7 +187,9 @@
Object value = parseValue();
if (value == null) {
- throw new ParseException("Bad value associated
with key " + key, tokenizer.lineno());
+ throw new ParseException(
+ "Bad value associated with key
" + key, tokenizer
+ .lineno());
}
result.add(new KeyValue(key, value));
@@ -224,47 +214,45 @@
}
/**
- * An integer consists of hte characters [0-9]
- * Assuming hte precondition that we have already checked
- * for the end of file
+ * An integer consists of hte characters [0-9] Assuming hte precondition
+ * that we have already checked for the end of file
*/
private boolean isInteger() {
return integerPattern.matcher(tokenizer.sval).matches();
}
/**
- * A real consists of 1 or more digits followed by a ., followed by one
or more digits
- * and an optional mantissa. Assuming the preconiditon that we have
already
- * checked for hte end of file
+ * A real consists of 1 or more digits followed by a ., followed by one
or
+ * more digits and an optional mantissa. Assuming the preconiditon that
we
+ * have already checked for hte end of file
*/
private boolean isReal() {
return realPattern.matcher(tokenizer.sval).matches();
}
/**
- * A string consits of a string that begins and ends with the quote
character
- * The streamtokenizer will basically check for this for me, so I just
- * have to check the token type and see if it is a quote char
- * It's also not supposed ot have a couple things in it, but I don't
really
- * have a check for that.
+ * A string consits of a string that begins and ends with the quote
+ * character The streamtokenizer will basically check for this for me,
so I
+ * just have to check the token type and see if it is a quote char It's
also
+ * not supposed ot have a couple things in it, but I don't really have a
+ * check for that.
*/
private boolean isString() {
return tokenizer.ttype == QUOTE_CHAR;
}
/**
- * A list starts with the list open character
- * I'm assuming I get some white space before and
- * after the list delimiter, that might not actually
- * be true according to the spec
+ * A list starts with the list open character I'm assuming I get some
white
+ * space before and after the list delimiter, that might not actually be
+ * true according to the spec
*/
private boolean isList() {
return tokenizer.sval.equals(LIST_OPEN);
}
/**
- * Verify that the current value is a key,
- * and then return the key that is found
+ * Verify that the current value is a key, and then return the key that
is
+ * found
*/
private String parseKey() {
if (isKey()) {
@@ -275,8 +263,8 @@
}
/**
- * Parse out a value, it can be a integer,real,string, or a list.
Assume is has already been found
- * to not be the end of file
+ * Parse out a value, it can be a integer,real,string, or a list.
Assume is
+ * has already been found to not be the end of file
*/
private Object parseValue() throws IOException, ParseException {
Object result = null;
@@ -303,7 +291,8 @@
List list = parseList();
if (!tokenizer.sval.equals(LIST_CLOSE)) {
- throw new ParseException("Unterminated list",
tokenizer.lineno());
+ throw new ParseException("Unterminated list",
tokenizer
+ .lineno());
}
return list;
@@ -315,10 +304,10 @@
/**
* This misery exists to overcome a bug in the java.io.StreamTokenizer
lib.
* the problem is that StreamTokenizer treats newlines as end-of-quotes,
- * which means you can't have quoted strings over multiple lines. This,
- * however, violates the GML grammar. So, since the grammar treats
newlines
- * and spaces the same, we just turn all newlines and carriage returns
- * into spaces. Fortunately for us, StreamTokenizer only calls the
read() method.
+ * which means you can't have quoted strings over multiple lines. This,
+ * however, violates the GML grammar. So, since the grammar treats
newlines
+ * and spaces the same, we just turn all newlines and carriage returns
into
+ * spaces. Fortunately for us, StreamTokenizer only calls the read()
method.
*/
private class FilterNewlineReader extends FilterReader {
public FilterNewlineReader(Reader r) {
Modified: cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
19:25:15 UTC (rev 19070)
+++ cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
19:53:58 UTC (rev 19071)
@@ -36,59 +36,44 @@
*/
package cytoscape.data.readers;
-import cern.colt.list.IntArrayList;
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.NodeView;
-import cern.colt.map.OpenIntIntHashMap;
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+import cern.colt.list.IntArrayList;
+import cern.colt.map.OpenIntIntHashMap;
import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
-
import cytoscape.data.CyAttributes;
import cytoscape.data.Semantics;
-
import cytoscape.init.CyInitParams;
-
import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.LayoutAdapter;
-
import cytoscape.logger.CyLogger;
-
import cytoscape.task.TaskMonitor;
-
import cytoscape.util.FileUtil;
import cytoscape.util.PercentUtil;
-
import cytoscape.view.CyNetworkView;
-
import cytoscape.visual.ArrowShape;
-import cytoscape.visual.LineStyle;
import cytoscape.visual.NodeShape;
-import cytoscape.visual.VisualMappingManager;
import cytoscape.visual.VisualPropertyType;
-import giny.model.Edge;
-import giny.model.Node;
-import giny.view.EdgeView;
-import giny.view.GraphView;
-import giny.view.NodeView;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import java.io.InputStream;
-import java.io.StringWriter;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-
/**
* This class is responsible for converting a gml object tree into cytoscape
* objects New features to the current version: 1. Small bug fixes. 2.
Translate
@@ -108,74 +93,75 @@
*/
// Graph Tags
- protected static String GRAPH = "graph";
- protected static String NODE = "node";
- protected static String EDGE = "edge";
- protected static String GRAPHICS = "graphics";
- protected static String LABEL = "label";
- protected static String SOURCE = "source";
- protected static String TARGET = "target";
+ protected static final String GRAPH = "graph";
+ protected static final String NODE = "node";
+ protected static final String EDGE = "edge";
+ protected static final String GRAPHICS = "graphics";
+ protected static final String LABEL = "label";
+ protected static final String SOURCE = "source";
+ protected static final String TARGET = "target";
// The following elements are in "graphics" section of GML
- protected static String X = "x";
- protected static String Y = "y";
- protected static String H = "h";
- protected static String W = "w";
- protected static String TYPE = "type";
- protected static String ID = "id";
- protected static String ROOT_INDEX = "root_index";
+ protected static final String X = "x";
+ protected static final String Y = "y";
+ protected static final String H = "h";
+ protected static final String W = "w";
+ protected static final String TYPE = "type";
+ protected static final String ID = "id";
+ protected static final String ROOT_INDEX = "root_index";
// Shapes used in Cytoscape (not GML standard)
// In GML, they are called "type"
- protected static String RECTANGLE = "rectangle";
- protected static String ELLIPSE = "ellipse";
- protected static String LINE = "Line"; // This is the Polyline object.
+ protected static final String RECTANGLE = "rectangle";
+ protected static final String ELLIPSE = "ellipse";
+ protected static final String LINE = "Line"; // This is the Polyline
object.
// no support for now...
- protected static String POINT = "point";
- protected static String DIAMOND = "diamond";
- protected static String HEXAGON = "hexagon";
- protected static String OCTAGON = "octagon";
- protected static String PARALELLOGRAM = "parallelogram";
- protected static String TRIANGLE = "triangle";
+ protected static final String POINT = "point";
+ protected static final String DIAMOND = "diamond";
+ protected static final String HEXAGON = "hexagon";
+ protected static final String OCTAGON = "octagon";
+ protected static final String PARALELLOGRAM = "parallelogram";
+ protected static final String TRIANGLE = "triangle";
// Other GML "graphics" attributes
- protected static String FILL = "fill";
- protected static String WIDTH = "width";
- protected static String STRAIGHT_LINES = "line";
- protected static String CURVED_LINES = "curved";
- protected static String SOURCE_ARROW = "source_arrow";
- protected static String TARGET_ARROW = "target_arrow";
+ protected static final String FILL = "fill";
+ protected static final String WIDTH = "width";
+ protected static final String STRAIGHT_LINES = "line";
+ protected static final String CURVED_LINES = "curved";
+ protected static final String SOURCE_ARROW = "source_arrow";
+ protected static final String TARGET_ARROW = "target_arrow";
// Support for yEd GML dialect
- protected static String YED_SOURCE_ARROW = "sourceArrow";
- protected static String YED_TARGET_ARROW = "targetArrow";
- protected static String YED_DELTA = "delta";
- protected static String YED_STANDARD = "standard";
- protected static String YED_DIAMOND = "diamond";
- protected static String YED_SHORT = "short";
- protected static String YED_WHITE_DELTA = "white_delta";
- protected static String YED_WHITE_DIAMOND = "white_diamond";
+ protected static final String YED_SOURCE_ARROW = "sourceArrow";
+ protected static final String YED_TARGET_ARROW = "targetArrow";
+ protected static final String YED_DELTA = "delta";
+ protected static final String YED_STANDARD = "standard";
+ protected static final String YED_DIAMOND = "diamond";
+ protected static final String YED_SHORT = "short";
+ protected static final String YED_WHITE_DELTA = "white_delta";
+ protected static final String YED_WHITE_DIAMOND = "white_diamond";
// States of the ends of arrows
- protected static String ARROW = "arrow";
- protected static String ARROW_NONE = "none";
- protected static String ARROW_FIRST = "first";
- protected static String ARROW_LAST = "last";
- protected static String ARROW_BOTH = "both";
- protected static String OUTLINE = "outline";
- protected static String OUTLINE_WIDTH = "outline_width";
- protected static String DEFAULT_EDGE_INTERACTION = "pp";
- protected static String VERSION = "Version";
- protected static String CREATOR = "Creator";
- private String mapSuffix;
- private Color DEF_COLOR = new Color(153, 153, 255);
+ protected static final String ARROW = "arrow";
+ protected static final String ARROW_NONE = "none";
+ protected static final String ARROW_FIRST = "first";
+ protected static final String ARROW_LAST = "last";
+ protected static final String ARROW_BOTH = "both";
+ protected static final String OUTLINE = "outline";
+ protected static final String OUTLINE_WIDTH = "outline_width";
+ protected static final String DEFAULT_EDGE_INTERACTION = "pp";
+ protected static final String VERSION = "Version";
+ protected static final String CREATOR = "Creator";
+
+ private static final Color DEF_COLOR = new Color(153, 153, 255);
+
private String vsbSwitch =
CytoscapeInit.getProperties().getProperty("visualStyleBuilder");
private VisualStyleBuilder graphStyle = null;
- protected static CyLogger logger = CyLogger.getLogger(GMLReader.class);
+ private static CyLogger logger = CyLogger.getLogger(GMLReader.class);
// Entries in the file
- List keyVals;
+ private List<KeyValue> keyVals;
// Node ID's
OpenIntIntHashMap nodeIDMap;
@@ -227,7 +213,7 @@
*
* @param filename File name.
*/
- public GMLReader(String filename) {
+ public GMLReader(final String filename) {
this(filename, null);
}
@@ -239,7 +225,7 @@
* Input stream of GML file,
*
*/
- public GMLReader(InputStream is, String name) {
+ public GMLReader(final InputStream is, final String name) {
super(name);
// Set new style name
@@ -256,7 +242,7 @@
* @param filename File name.
* @param taskMonitor TaskMonitor Object.
*/
- public GMLReader(String filename, TaskMonitor taskMonitor) {
+ public GMLReader(final String filename, final TaskMonitor taskMonitor) {
super(filename);
inputStream = FileUtil.getInputStream(filename);
@@ -282,111 +268,30 @@
}
private String createVSName() {
- // Create new style name
- // String target = null;
-
- // File fileTest = new File(fileName);
- // target = fileTest.getName();
- // logger.info("Target GML file is " + fileName);
- mapSuffix = " for " + fileName;
-
- return getNetworkName(); //fileName.concat("_GML_style");
+ return getNetworkName() + " Style";
}
private void initializeHash() {
- // Initialize HashMap for new visual style
- //nodeW = new HashMap();
- //nodeH = new HashMap();
- //nodeShape = new HashMap<String,NodeShape>();
- //nodeCol = new HashMap();
- //nodeBWidth = new HashMap<String,Double>();
- //nodeBCol = new HashMap();
- //edgeCol = new HashMap();
- //edgeWidth = new HashMap<String,Float>();
- //edgeArrow = new HashMap<String,String>();
- //edgeShape = new HashMap();
edge_names = new Vector();
node_names = new Vector();
}
+
// Initialize variables for the new style created from GML
- //
private void initStyle() {
graphStyle = new VisualStyleBuilder(styleName, false);
graphStyle.setNodeSizeLocked(false);
}
- // Create maps for the node attribute and set it as a Visual Style.
- /**
- * DOCUMENT ME!
- *
- * @param vizmapper DOCUMENT ME!
- * @deprecated Don't use this. Gone 2/2009.
- */
- @Deprecated
- public void setNodeMaps(VisualMappingManager vizmapper) {
- }
- //
/**
- * DOCUMENT ME!
- *
- * @param vizmapper DOCUMENT ME!
- * @deprecated Don't use this. Gone 2/2009.
+ * Read GML file contents
*/
- @Deprecated
- public void setEdgeMaps(VisualMappingManager vizmapper) {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param mapSuffix DOCUMENT ME!
- * @param VSName DOCUMENT ME!
- * @deprecated Don't use this. Gone 2/2009.
- */
- @Deprecated
- public void applyMaps(String mapSuffix, String VSName) {
- // CytoscapeDesktop cyDesktop = Cytoscape.getDesktop();
- // VisualMappingManager vizmapper =
cyDesktop.getVizMapManager();
- /*
- if (VSName != null) {
- styleName = VSName;
- }
-
- if (mapSuffix != null) {
- this.mapSuffix = mapSuffix;
- }
-
- VisualMappingManager vizmapper =
Cytoscape.getVisualMappingManager();
- catalog = vizmapper.getCalculatorCatalog();
-
- setNodeMaps(vizmapper);
- setEdgeMaps(vizmapper);
-
- //
- // Create new VS and apply it
- //
- gac.setDefaultBackgroundColor(DEF_COLOR);
- gmlstyle = new VisualStyle(styleName, nac, eac, gac);
-
- catalog.addVisualStyle(gmlstyle);
- vizmapper.setVisualStyle(gmlstyle);
-
- Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
- */
- }
-
- //
- /**
- * DOCUMENT ME!
- */
public void read() {
try {
try {
keyVals = (new GMLParser(inputStream)).parseList();
- }
- finally {
+ } finally {
if (inputStream != null) {
inputStream.close();
}
@@ -570,10 +475,8 @@
* This function takes in a list which was given as the value to a
"graph"
* key underneath the main gml list
*/
- protected void readGraph(List list) {
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
+ protected void readGraph(final List<KeyValue> list) {
+ for (KeyValue keyVal: list) {
if (keyVal.key.equals(NODE)) {
readNode((List) keyVal.value);
}
@@ -1219,8 +1122,8 @@
*
* @param net DOCUMENT ME!
*/
- public void doPostProcessing(CyNetwork net) {
- //
+ public void doPostProcessing(final CyNetwork net) {
+
CyInitParams init = CytoscapeInit.getCyInitParams();
if (init == null)
Modified: cytoscape/trunk/src/cytoscape/data/readers/KeyValue.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/KeyValue.java 2010-01-29
19:25:15 UTC (rev 19070)
+++ cytoscape/trunk/src/cytoscape/data/readers/KeyValue.java 2010-01-29
19:53:58 UTC (rev 19071)
@@ -33,31 +33,27 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
package cytoscape.data.readers;
-
/**
- *
+ * Key and Value pair in GML file.
*/
public class KeyValue {
- /**
- *
- */
- public String key;
- /**
- *
- */
+ // These are immutable.
+ public final String key;
public Object value;
/**
* Creates a new KeyValue object.
- *
- * @param key DOCUMENT ME!
- * @param value DOCUMENT ME!
+ *
+ * @param key
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
*/
- public KeyValue(String key, Object value) {
+ public KeyValue(final String key, final Object value) {
this.key = key;
this.value = value;
}
Modified: cytoscape/trunk/src/cytoscape/visual/AppearanceCalculator.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/AppearanceCalculator.java
2010-01-29 19:25:15 UTC (rev 19070)
+++ cytoscape/trunk/src/cytoscape/visual/AppearanceCalculator.java
2010-01-29 19:53:58 UTC (rev 19071)
@@ -80,12 +80,11 @@
if (toCopy == null)
return;
- for (Calculator c : toCopy.getCalculators()) {
- CyLogger.getLogger().info("New calc = " + c.toString());
+ for (Calculator c : toCopy.getCalculators())
setCalculator(c);
- }
- deps.copy( toCopy.deps );
+ if (deps != null)
+ deps.copy( toCopy.deps );
copyDefaultAppearance(toCopy);
}
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