Author: mes
Date: 2011-01-25 13:31:02 -0800 (Tue, 25 Jan 2011)
New Revision: 23611
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
Log:
fixed attr reader
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
2011-01-25 21:24:09 UTC (rev 23610)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
2011-01-25 21:31:02 UTC (rev 23611)
@@ -19,6 +19,7 @@
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
+import java.util.List;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
@@ -28,36 +29,25 @@
import java.util.Iterator;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.io.read.CyTableReader;
+import org.cytoscape.task.table.MapNetworkAttrTask;
+import org.cytoscape.work.AbstractTask;
-public class CyAttributesReader implements CyTableReader {
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+public class CyAttributesReader extends AbstractTask implements CyTableReader {
- /**
- * This type corresponds to java.lang.Boolean.
- */
- public final byte TYPE_BOOLEAN = 1;
- /**
- * This type corresponds to java.lang.Double.
- */
- public final byte TYPE_FLOATING_POINT = 2;
+ private static final Logger logger =
LoggerFactory.getLogger(CyAttributesReader.class);
- /**
- * This type corresponds to java.lang.Integer.
- */
+ public final byte TYPE_BOOLEAN = 1;
+ public final byte TYPE_FLOATING_POINT = 2;
public final byte TYPE_INTEGER = 3;
-
- /**
- * This type corresponds to java.lang.String.
- */
public final byte TYPE_STRING = 4;
-
public static final String ENCODING_SCHEME = "UTF-8";
-
- ////////////////////
-
public static final String DECODE_PROPERTY =
"cytoscape.decode.attributes";
private static final String badDecodeMessage =
"Trouble when decoding attribute value, first occurence line
no. {0}" +
@@ -67,84 +57,55 @@
private boolean badDecode;
private int lineNum;
private boolean doDecoding;
- final Map<String, Map<String, Class>> idsToAttribNameToTypeMapMap;
- //private final CyLogger logger;
private CyTableManager tableMgr;
private CyTableFactory tableFactory;;
private InputStream inputStream;
- private CyTable[] cyTables = null;
- private CyNetwork[] networks= null;
- private String nodeOrEdge; //node or edge
- private String globalTableTitle = "ThisIsAGlobalTable";// This will be
replaced by the "file name" later
+ private CyTable[] cyTables;
private CyApplicationManager appMgr;
private CyNetworkManager netMgr;
- private CyTable globalTable = null;
-
+
@Tunable(description = "Select Data Type")
public final ListSingleSelection<String> dataTypeOptions;
+
+ private static int numImports = 0;
- @Tunable(description = "Select Network")
- public final ListSingleSelection<String> networkOptions;
-
-
public CyAttributesReader(InputStream inputStream, CyTableFactory
tableFactory, CyTableManager tableMgr,
CyApplicationManager appMgr, CyNetworkManager netMgr) {
- //logger = CyLogger.getLogger(CyAttributesReader.class);
lineNum = 0;
doDecoding =
Boolean.valueOf(System.getProperty(DECODE_PROPERTY, "true"));
- idsToAttribNameToTypeMapMap = new HashMap<String, Map<String,
Class>>();
this.tableMgr = tableMgr;
this.tableFactory = tableFactory;
this.appMgr = appMgr;
this.netMgr = netMgr;
-
this.inputStream = inputStream;
- ArrayList<String> options1 = new ArrayList<String>();
- options1.add("Node");
- options1.add("Edge");
-
+ List<String> options1 = new ArrayList<String>();
+ if ( netMgr.getNetworkSet().size() > 0 ) {
+ options1.add("Node");
+ options1.add("Edge");
+ options1.add("Network");
+ options1.add("Unbound");
+ } else {
+ options1.add("Unbound");
+ }
+
dataTypeOptions = new ListSingleSelection<String>(options1);
-
- ArrayList<String> options2 = new ArrayList<String>();
- options2.add("Current network");
- options2.add("All networks");
- options2.add("No network");
-
- networkOptions = new ListSingleSelection<String>(options2);
}
@Override
public void run(TaskMonitor tm) throws IOException {
- if
(dataTypeOptions.getSelectedValue().equalsIgnoreCase("Node")){
- nodeOrEdge = "node";
- }
- else { // Edge
- nodeOrEdge = "edge";
- }
-
- ////
- String networkType = networkOptions.getSelectedValue();
-
- if (networkType.equalsIgnoreCase("Current network")){
- networks = new CyNetwork[1];//
- networks[0] = this.appMgr.getCurrentNetwork();
- }
- else if (networkType.equalsIgnoreCase("All networks")){
- networks =
(CyNetwork[])netMgr.getNetworkSet().toArray();
- }
- else { // no network yet, its global attribute
- networks = null;
- }
-
- ///
+
+ CyTable table = tableFactory.createTable("AttrTable " +
Integer.toString(numImports++),
+ "name",
String.class, true);
+ cyTables = new CyTable[] { table };
+
try {
- loadAttributesInternal();
+ loadAttributesInternal(table);
} finally {
if (inputStream != null) {
inputStream.close();
@@ -152,39 +113,26 @@
}
}
- tm.setProgress(1.0);
+ Class<? extends CyTableEntry> type = getMappingClass();
+
+ if ( netMgr.getNetworkSet().size() > 0 && type != null )
+ super.insertTasksAfterCurrentTask( new
MapNetworkAttrTask(type,table,netMgr,appMgr) );
}
-
- /*
- private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
- switch (attribType) {
- case CyAttributes.TYPE_BOOLEAN:
- return Boolean.class;
- case CyAttributes.TYPE_INTEGER:
- return Long.class;
- case CyAttributes.TYPE_FLOATING:
- return Double.class;
- case CyAttributes.TYPE_STRING:
- return String.class;
- case CyAttributes.TYPE_SIMPLE_LIST:
- return List.class;
- default:
- return null;
- }
+ private Class<? extends CyTableEntry> getMappingClass() {
+ String sel = dataTypeOptions.getSelectedValue();
+ if ( sel.equals("Node") )
+ return CyNode.class;
+ else if ( sel.equals("Edge") )
+ return CyEdge.class;
+ else if ( sel.equals("Network") )
+ return CyNetwork.class;
+ else
+ return null;
}
- */
+
-
- /**
- * DOCUMENT ME!
- *
- * @param cyAttrs DOCUMENT ME!
- * @param fileIn DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
- */
- private void loadAttributesInternal() throws IOException
+ private void loadAttributesInternal(CyTable table) throws IOException
{
InputStreamReader reader1 = new
InputStreamReader(this.inputStream);
@@ -324,8 +272,7 @@
}
}
- //cyAttrs.setListAttribute(key,
attributeName, elmsBuff);
- setListArrtibute(type, key,
attributeName, elmsBuff);
+ setListArrtibute(table, type, key,
attributeName, elmsBuff);
} else { // Not a list.
@@ -359,57 +306,9 @@
firstLine = false;
}
-
- if (networks != null){
- // Load attributes for current
network or all networks there
- setAttributeForType(type, key,
attributeName, val);
- }
- else { // networks = null, load the
attribute into global table
-
- // If globalTable does not
exist, create it
- if (globalTable == null){
- String primaryKey =
"ID";
- globalTable =
tableFactory.createTable(this.globalTableTitle, primaryKey, String.class, true);
- }
-
- // key, attributeName, val
- // If the column does not
exist, create it
- if
(globalTable.getColumnTypeMap().get(attributeName)== null)
- {
- if (type ==
TYPE_INTEGER){
-
globalTable.createColumn(attributeName, Integer.class);
- }
- else if (type ==
TYPE_BOOLEAN){
-
globalTable.createColumn(attributeName, Boolean.class);
- }
- else if (type ==
TYPE_FLOATING_POINT){
-
globalTable.createColumn(attributeName, Double.class);
- }
- else { // String
-
globalTable.createColumn(attributeName, String.class);
- }
- }
-
- // Now add the attributes for
the row based on the key
- CyRow row =
globalTable.getRow(key);
-
- if (type == TYPE_INTEGER){
- row.set(attributeName,
new Integer(val));
- }
- else if (type == TYPE_BOOLEAN){
- row.set(attributeName,
new Boolean(val));
- }
- else if (type ==
TYPE_FLOATING_POINT){
- row.set(attributeName,
new Double(val));
- }
- else { // String
- row.set(attributeName,
new String(val));
- }
- }
-
+ setAttributeForType(table, type, key,
attributeName, val);
}
-
- }// End of while loop
+ }
} catch (Exception e) {
String message;
if (guessedAttrType) {
@@ -424,144 +323,64 @@
else
message = "failed parsing attributes file at
line: " + lineNum
+ " with exception: " + e.getMessage();
- //logger.warn(message, e);
+ logger.warn(message, e);
throw new IOException(message);
}
}
- private void setAttributeForType(byte type, String key, String
attributeName, String val){
+ private void setAttributeForType(CyTable tbl, byte type, String key,
String attributeName, String val){
- for (int i= 0; i< networks.length; i++){
- Map<String, CyTable> map;
- if (nodeOrEdge.equalsIgnoreCase("Node")){
- map = tableMgr.getTableMap(CyNode.class,
networks[i]);
+ if (!tbl.getColumnTypeMap().keySet().contains(attributeName))
+ {
+ if (type == TYPE_INTEGER){
+ tbl.createColumn(attributeName, Integer.class);
}
- else {
- map = tableMgr.getTableMap(CyEdge.class,
networks[i]);
+ else if (type == TYPE_BOOLEAN){
+ tbl.createColumn(attributeName, Boolean.class);
}
-
- CyTable tbl = map.get(CyNetwork.DEFAULT_ATTRS);
-
- if
(!tbl.getColumnTypeMap().keySet().contains(attributeName))
- {
- if (type == TYPE_INTEGER){
- tbl.createColumn(attributeName,
Integer.class);
- }
- else if (type == TYPE_BOOLEAN){
- tbl.createColumn(attributeName,
Boolean.class);
- }
- else if (type == TYPE_FLOATING_POINT) {
- tbl.createColumn(attributeName,
Double.class);
- }
- else { // type is String
- tbl.createColumn(attributeName,
String.class);
- }
+ else if (type == TYPE_FLOATING_POINT) {
+ tbl.createColumn(attributeName, Double.class);
}
-
- Set<CyRow> rows = tbl.getMatchingRows("name", key);
-
- Iterator<CyRow> it = rows.iterator();
- while (it.hasNext()){
- CyRow row = it.next();
- if (type == TYPE_INTEGER){
- row.set(attributeName, new
Integer(val));
- }
- else if (type == TYPE_BOOLEAN){
- row.set(attributeName, new
Boolean(val));
- }
- else if (type == TYPE_FLOATING_POINT) {
- row.set(attributeName, (new
Double(val)));
- }
- else {// type is String
- row.set(attributeName, new String(val));
- }
+ else { // type is String
+ tbl.createColumn(attributeName, String.class);
}
}
+
+ CyRow row = tbl.getRow(key);
+
+ if (type == TYPE_INTEGER){
+ row.set(attributeName, new Integer(val));
+ }
+ else if (type == TYPE_BOOLEAN){
+ row.set(attributeName, new Boolean(val));
+ }
+ else if (type == TYPE_FLOATING_POINT) {
+ row.set(attributeName, (new Double(val)));
+ }
+ else {// type is String
+ row.set(attributeName, new String(val));
+ }
}
- private void setListArrtibute(Byte type, String key, String
attributeName, final ArrayList elmsBuff){
+ private void setListArrtibute(CyTable tbl, Byte type, String key,
String attributeName, final ArrayList elmsBuff){
- // Load global attribute
- if (networks == null){
- // If globalTable does not exist, create it
- if (globalTable == null){
- String primaryKey = "ID";
- globalTable =
tableFactory.createTable(this.globalTableTitle, primaryKey, String.class, true);
- }
-
- // key, attributeName, val
- // If the column does not exist, create it
- if (globalTable.getColumnTypeMap().get(attributeName)==
null)
- {
- if (type == TYPE_INTEGER){
-
globalTable.createListColumn(attributeName, Integer.class);
- }
- else if (type == TYPE_BOOLEAN){
-
globalTable.createListColumn(attributeName, Boolean.class);
- }
- else if (type == TYPE_FLOATING_POINT){
-
globalTable.createListColumn(attributeName, Double.class);
- }
- else { // String
-
globalTable.createListColumn(attributeName, String.class);
- }
- }
-
- // Now add the attributes for the row based on the key
- CyRow row = globalTable.getRow(key);
-
+ if (!tbl.getColumnTypeMap().keySet().contains(attributeName))
+ {
if (type == TYPE_INTEGER){
- row.set(attributeName, elmsBuff);
+ tbl.createListColumn(attributeName,
Integer.class);
}
else if (type == TYPE_BOOLEAN){
- row.set(attributeName, elmsBuff);
+ tbl.createListColumn(attributeName,
Boolean.class);
}
- else if (type == TYPE_FLOATING_POINT){
- row.set(attributeName, elmsBuff);
+ else if (type == TYPE_FLOATING_POINT) {
+ tbl.createListColumn(attributeName,
Double.class);
}
- else { // String
- row.set(attributeName, elmsBuff);
+ else { // type is String, do nothing
}
-
- return;
}
-
- // networks != null
- ////////Load network-specific attributes ////////
- for (int i= 0; i< networks.length; i++){
- Map<String, CyTable> map;
- if (nodeOrEdge.equalsIgnoreCase("Node")){
- map = tableMgr.getTableMap(CyNode.class,
networks[i]);
- }
- else {// Edge
- map = tableMgr.getTableMap(CyEdge.class,
networks[i]);
- }
- CyTable tbl = map.get(CyNetwork.DEFAULT_ATTRS);
-
- if
(!tbl.getColumnTypeMap().keySet().contains(attributeName))
- {
- if (type == TYPE_INTEGER){
- tbl.createListColumn(attributeName,
Integer.class);
- }
- else if (type == TYPE_BOOLEAN){
- tbl.createListColumn(attributeName,
Boolean.class);
- }
- else if (type == TYPE_FLOATING_POINT) {
- tbl.createListColumn(attributeName,
Double.class);
- }
- else { // type is String, do nothing
- }
- }
-
- Set<CyRow> rows = tbl.getMatchingRows("name", key);
-
- Iterator<CyRow> it = rows.iterator();
- while (it.hasNext()){
- CyRow row = it.next();
- row.set(attributeName, elmsBuff);
- }
- }
+ CyRow row = tbl.getRow(key);
+ row.set(attributeName, elmsBuff);
}
@@ -625,34 +444,9 @@
public void setDoDecoding(boolean doDec) {
doDecoding = doDec;
}
-
- public CyTable[] getCyTables(){
- //Gloal table
- if (networks == null){
- cyTables = new CyTable[] { this.globalTable };
- return cyTables;
- }
- //network-specific tables
- cyTables = new CyTable[networks.length];
- if (this.nodeOrEdge.equalsIgnoreCase("Node")){
- for (int i=0; i< networks.length; i++){
- Map<String, CyTable> map =
tableMgr.getTableMap(CyNode.class, networks[i]);
- CyTable tbl = map.get(CyNetwork.DEFAULT_ATTRS);
- cyTables[i] = tbl;
- }
- }
- else {// Edge
- for (int i=0; i< networks.length; i++){
- Map<String, CyTable> map =
tableMgr.getTableMap(CyEdge.class, networks[i]);
- CyTable tbl = map.get(CyNetwork.DEFAULT_ATTRS);
- cyTables[i] = tbl;
- }
- }
-
+ @Override
+ public CyTable[] getCyTables(){
return cyTables;
}
-
- public void cancel(){
- }
}
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