Author: jgao
Date: 2011-08-09 19:42:05 -0700 (Tue, 09 Aug 2011)
New Revision: 26525
Removed:
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/AttributeValueCastUtils.java
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/CopyingAttributeValueVisitor.java
Log:
Network merge: remove old code
Deleted:
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/AttributeValueCastUtils.java
===================================================================
---
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/AttributeValueCastUtils.java
2011-08-10 01:58:34 UTC (rev 26524)
+++
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/AttributeValueCastUtils.java
2011-08-10 02:42:05 UTC (rev 26525)
@@ -1,235 +0,0 @@
-/* File: AbstractNetworkMerge.java
-
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- 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 org.cytoscape.network.merge.internal.util;
-
-
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.List;
-import java.util.HashSet;
-
-import org.cytoscape.model.CyTable;
-
-/**
- *
- *
- */
-public class AttributeValueCastUtils {
- /**
- * Check if the types are convertable for two attributes
- * @param fromAttrName
- * @param toAttrName
- * @param attrs
- * @return
- */
- public static boolean isAttributeTypeConvertable(final String
fromAttrName,
- final String toAttrName,
- final CyTable attrs) {
- if (fromAttrName==null || toAttrName==null || attrs==null) {
- throw new java.lang.NullPointerException("Null fromAttrName or
toAttrName or attrs");
- }
-
- final Set<String> attrNames = attrs.getColumnTypeMap().keySet();
- if (!attrNames.contains(fromAttrName)) {
- throw new java.lang.IllegalArgumentException("'"+fromAttrName+"'
not exists");
- }
-
- if (!attrNames.contains(toAttrName)) {
- return true; // always convertible to a non-existing attribute
- }
-
- // first check the basic type is convertible
- final Class<?> valType1 = attrs.getType(fromAttrName);
- final Class<?> valType2 = attrs.getType(toAttrName);
-
- if (valType1 != valType2) { // if value type is not the same
- if ( valType1 == Boolean.class ) {
- if (valType2!=Boolean.class && valType2!=String.class) {
- return false;
- }
- } else if ( valType1 == Double.class ) {
- if (valType2!=Double.class && valType2!=String.class) {
- return false;
- }
- } else if ( valType1 == Integer.class) {
- if (valType2!=Integer.class && valType2!=Double.class &&
valType2!=String.class) {
- return false;
- }
- } else if ( valType1 == String.class ) {
- if (valType2!=String.class) {
- return false;
- }
- } else {
- return false;
- }
- }
-
- // TODO figure out what to do with lists and maps!
- // check list, map ...
-// final byte[] dimTypes1 =
mmapDef.getAttributeKeyspaceDimensionTypes(fromAttrName);
-// final byte[] dimTypes2 =
mmapDef.getAttributeKeyspaceDimensionTypes(toAttrName);
-//
-// final int n1 = dimTypes1.length;
-// final int n2 = dimTypes2.length;
-//
-// if (n2==0 && valType2==MultiHashMapDefinition.TYPE_STRING) {
-// return true; // any type can convert to String
-// }
-//
-// if (n1==0 && n2==0) { // simple types
-// return true;
-// }
-//
-// if (n1==0 && n2==1) {
-// return dimTypes2[0] == MultiHashMapDefinition.TYPE_INTEGER; //
converting from simple type to simple list
-// }
-//
-// if (n1!=n2) {
-// return false;
-// }
-//
-// for (int i=0; i<n1; i++) {
-// if (dimTypes1[i]!=dimTypes2[i]) {
-// return false;
-// }
-// }
-
- return valType1==valType2; // for complex case, type must be the same
- }
-
- public static boolean isAttributeTypeConvertable(final Class<?>
fromType,
- final Class<?> toType) {
- if (fromType == Boolean.class) {
- return toType == Boolean.class || toType ==
String.class;
- // || toType==CyAttributes.TYPE_SIMPLE_LIST;
- } else if (fromType == Double.class) {
- return toType == Double.class || toType == String.class;
- // || toType==CyAttributes.TYPE_SIMPLE_LIST;
- } else if (fromType == Integer.class) {
- return toType == Integer.class || toType == Double.class
- || toType == String.class;
- // || toType==CyAttributes.TYPE_SIMPLE_LIST;
- } else if (fromType == String.class) {
- return toType == String.class;
- // || toType==CyAttributes.TYPE_SIMPLE_LIST;
- // } else if ( fromType ==
CyAttributes.TYPE_SIMPLE_LIST ) {
- // return toType==String.class
- // || toType==CyAttributes.TYPE_SIMPLE_LIST;
- // } else if ( fromType ==
CyAttributes.TYPE_SIMPLE_MAP) {
- // return toType==CyAttributes.TYPE_STRING
- // || toType==CyAttributes.TYPE_SIMPLE_MAP;
- // } else if ( fromType == CyAttributes.TYPE_COMPLEX ) {
- // return toType==CyAttributes.TYPE_STRING
- // || toType==CyAttributes.TYPE_SIMPLE_MAP;
- } else {
- return false;
- }
- }
-
- /*
- * Return the attribute with the highest compatible attribute
- *
- */
- public static String getMostCompatibleAttribute(final Set<String>
attrNames, final CyTable attrs) {
- if (attrNames==null || attrs==null) {
- throw new java.lang.NullPointerException("Null attrNames or
attrs");
- }
-
- attrNames.remove(null);
- if (attrNames.isEmpty()) {
- throw new java.lang.IllegalArgumentException("Empty attrNames");
- }
-
- if (!attrs.getColumnTypeMap().keySet().containsAll(attrNames)) {
- throw new java.lang.IllegalStateException("Attribute not exists");
- }
-
- String[] attrArray = attrNames.toArray(new String[0]);
- Set<String> compatibleSet = new HashSet<String>();
-
- int n = attrArray.length;
- for (int i=0; i<n; i++) {
- String attr1 = attrArray[i];
-
- boolean compatible = true;
- for (int j=0; j<n; j++) {
- if (j==i) continue;
- String attr2 = attrArray[j];
- if (!AttributeValueCastUtils.isAttributeTypeConvertable(attr2,
attr1, attrs)) {
- compatible = false;
- break;
- }
- }
-
- if (compatible) {
- compatibleSet.add(attr1);
- }
- }
-
- if (compatibleSet.isEmpty()) {
- return null;
- }
-
- final Iterator<String> it = compatibleSet.iterator();
- while (it.hasNext()) {
- // if exists list, return it
- String attr = it.next();
- Class<?> type = attrs.getType(attr);
- if (type==List.class) {
- return attr;
- }
- }
- return compatibleSet.iterator().next();
-
- }
-
- public static Object attributeValueCast(Class<?> typeTo, Object value) {
- if (typeTo == Boolean.class) {
- return Boolean.valueOf(value.toString());
- } else if (typeTo == Integer.class) {
- return Integer.valueOf(value.toString());
- } else if (typeTo == Double.class) {
- return Double.valueOf(value.toString());
- } else if (typeTo == String.class) {
- return value.toString();
- } else {
- throw new IllegalStateException("wrong type");
- }
- }
-
-}
Deleted:
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/CopyingAttributeValueVisitor.java
===================================================================
---
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/CopyingAttributeValueVisitor.java
2011-08-10 01:58:34 UTC (rev 26524)
+++
core3/network-merge-impl/trunk/src/main/java/org/cytoscape/network/merge/internal/util/CopyingAttributeValueVisitor.java
2011-08-10 02:42:05 UTC (rev 26525)
@@ -1,74 +0,0 @@
-/* File: AbstractNetworkMerge.java
-
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- 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 org.cytoscape.network.merge.internal.util;
-
-
-import cytoscape.data.CyAttributes;
-import cytoscape.data.AttributeValueVisitor;
-
-import java.util.Arrays;
-/**
- *
- * @
- */
-
- // this is different from CopyingAttributeValueVisitor in CyAtributeUtil
- // the attributes copying from and to can be different
- /**
- * copy each attribute value from copyID to an
- * attribute value of copyAttribute associated with objTraversedCopyID.
- */
- public class CopyingAttributeValueVisitor implements AttributeValueVisitor
{
- private String toID;
- private String toAttrName;
-
- public CopyingAttributeValueVisitor(String toID, String toAttrName) {
- this.toID = toID;
- this.toAttrName = toAttrName;
- }
-
- //@Override
- public void visitingAttributeValue(String fromID, String attrName,
- CyAttributes attrs, Object[]
keySpace,
- Object visitedValue) {
- if
(!Arrays.asList(attrs.getAttributeNames()).contains(toAttrName)) { // if
toAttribute not exists
- throw new java.lang.IllegalStateException("'"+toAttrName+"'
must be defined before calling this method");
- }
-
- attrs.getMultiHashMap().setAttributeValue(toID, toAttrName,
visitedValue, keySpace);
- }
- }
--
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.
