Author: mes
Date: 2012-05-07 15:19:00 -0700 (Mon, 07 May 2012)
New Revision: 29140
Removed:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java.asdf
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java.asdf
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory.java.asdf
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
Log:
removed unused code
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-05-07 22:10:30 UTC (rev 29139)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-05-07 22:19:00 UTC (rev 29140)
@@ -145,7 +145,6 @@
BasicCyFileFilter pdfFilter = new BasicCyFileFilter(new
String[]{"pdf"}, new String[]{"image/pdf"}, "PDF File",DataCategory.IMAGE,
streamUtil);
BasicCyFileFilter psFilter = new BasicCyFileFilter(new
String[]{"ps"}, new String[]{"image/ps"}, "Post Script (PS)
File",DataCategory.IMAGE, streamUtil);
BasicCyFileFilter svgFilter = new BasicCyFileFilter(new
String[]{"svg"}, new String[]{"image/svg"}, "Scalable Vector Graphics (SVG)
File",DataCategory.IMAGE, streamUtil);
- BasicCyFileFilter textTableFilter = new BasicCyFileFilter(new
String[]{}, new String[]{"text/plain"}, "Any text file",DataCategory.TABLE,
streamUtil);
BasicCyFileFilter attrsFilter = new BasicCyFileFilter(new
String[]{"attrs"}, new String[]{"text/plain"}, "Any text
file",DataCategory.TABLE, streamUtil);
BasicCyFileFilter sifFilter = new BasicCyFileFilter(new
String[]{"sif"}, new String[]{"text/sif"}, "SIF files",DataCategory.NETWORK,
streamUtil);
BasicCyFileFilter csvFilter = new BasicCyFileFilter(new
String[]{"csv"}, new String[]{"text/plain"}, "CSV file",DataCategory.TABLE,
streamUtil);
Deleted:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java.asdf
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java.asdf
2012-05-07 22:10:30 UTC (rev 29139)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java.asdf
2012-05-07 22:19:00 UTC (rev 29140)
@@ -1,334 +0,0 @@
-/*
- File: CyAttributesReader.java
-
- Copyright (c) 2006, 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 cytoscape.data.readers;
-
-import org.cytoscape.model.CyRow;
-import org.cytoscape.attributes.MultiHashMapDefinition;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.Reader;
-import java.util.ArrayList;
-import java.util.StringTokenizer;
-
-
-// I hate writing parsing code. Grumble grumble grumble.
-/**
- *
- */
-public class CyAttributesReader {
- /**
- * DOCUMENT ME!
- *
- * @param cyAttrs DOCUMENT ME!
- * @param fileIn DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
- */
- public static void loadAttributes(CyAttributes cyAttrs, Reader fileIn)
- throws IOException {
- int lineNum = 0;
-
- try {
- final BufferedReader reader;
-
- if (fileIn instanceof BufferedReader) {
- reader = (BufferedReader) fileIn;
- } else {
- reader = new BufferedReader(fileIn);
- }
-
- String attributeName;
- byte type = -1;
-
- {
- final String firstLine = reader.readLine();
- lineNum++;
-
- if (firstLine == null) {
- return;
- }
-
- final String searchStr = "class=";
- final int inx = firstLine.indexOf(searchStr);
-
- if (inx < 0) {
- attributeName = firstLine.trim();
- } else {
- attributeName = firstLine.substring(0,
inx - 1).trim();
-
- String foo = firstLine.substring(inx);
- final StringTokenizer tokens = new
StringTokenizer(foo);
- foo = tokens.nextToken();
-
- String className =
foo.substring(searchStr.length()).trim();
-
- if (className.endsWith(")")) {
- className =
className.substring(0, className.length() - 1);
- }
-
- if
(className.equalsIgnoreCase("java.lang.String")
- ||
className.equalsIgnoreCase("String")) {
- type =
MultiHashMapDefinition.TYPE_STRING;
- } else if
(className.equalsIgnoreCase("java.lang.Boolean")
- ||
className.equalsIgnoreCase("Boolean")) {
- type =
MultiHashMapDefinition.TYPE_BOOLEAN;
- } else if
(className.equalsIgnoreCase("java.lang.Integer")
- ||
className.equalsIgnoreCase("Integer")) {
- type =
MultiHashMapDefinition.TYPE_INTEGER;
- } else if
(className.equalsIgnoreCase("java.lang.Double")
- ||
className.equalsIgnoreCase("Double")
- ||
className.equalsIgnoreCase("java.lang.Float")
- ||
className.equalsIgnoreCase("Float")) {
- type =
MultiHashMapDefinition.TYPE_FLOATING_POINT;
- }
- }
- }
-
- if (attributeName.indexOf("(") >= 0) {
- attributeName = attributeName.substring(0,
attributeName.indexOf("(")).trim();
- }
-
- boolean firstLine = true;
- boolean list = false;
-
- while (true) {
- final String line = reader.readLine();
- lineNum++;
-
- if (line == null) {
- break;
- }
-
- if ("".equals(line.trim())) {
- continue;
- }
-
- int inx = line.indexOf('=');
- final String key = line.substring(0,
inx).trim();
- String val = line.substring(inx + 1).trim();
-
- if (firstLine && val.startsWith("(")) {
- list = true;
- }
-
- if (list) {
- // Chop away leading '(' and trailing
')'.
- val = val.substring(1).trim();
- val = val.substring(0, val.length() -
1).trim();
-
- // Home-grown parsing (ughh) to handle
escape sequences.
- final ArrayList<Object> elmsBuff = new
ArrayList<Object>();
-
- while (val.length() > 0) {
- final StringBuilder elmBuff =
new StringBuilder();
- int inx2;
-
- for (inx2 = 0; inx2 <
val.length(); inx2++) {
- char ch =
val.charAt(inx2);
-
- if (ch == ':') {
- inx2++;
- inx2++;
-
- break;
- } else if (ch == '\\') {
- if ((inx2 + 1)
< val.length()) {
- inx2++;
-
- char
ch2 = val.charAt(inx2);
-
- if (ch2
== 'n') {
-
elmBuff.append('\n');
- } else
if (ch2 == 't') {
-
elmBuff.append('\t');
- } else
if (ch2 == 'b') {
-
elmBuff.append('\b');
- } else
if (ch2 == 'r') {
-
elmBuff.append('\r');
- } else
if (ch2 == 'f') {
-
elmBuff.append('\f');
- } else {
-
elmBuff.append(ch2);
- }
- } else {
- /* val
ends in '\' - just ignore it. */ }
- } else {
-
elmBuff.append(ch);
- }
- }
-
- elmsBuff.add(new
String(elmBuff));
- val = val.substring(inx2);
- }
-
- if (firstLine) {
- if (type < 0) {
- while (true) {
- try {
-
Integer.valueOf((String) elmsBuff.get(0));
- type =
MultiHashMapDefinition.TYPE_INTEGER;
-
- break;
- } catch
(Exception e) {
- }
-
- try {
- new
Double((String) elmsBuff.get(0));
- type =
MultiHashMapDefinition.TYPE_FLOATING_POINT;
-
- break;
- } catch
(Exception e) {
- }
-
- //
try {
- //
new Boolean((String) elmsBuff.get(0));
- //
type = MultiHashMapDefinition.TYPE_BOOLEAN;
- //
break; }
- //
catch (Exception e) {}
- type =
MultiHashMapDefinition.TYPE_STRING;
-
- break;
- }
- }
-
- firstLine = false;
- }
-
- for (int i = 0; i < elmsBuff.size();
i++) {
- if (type ==
MultiHashMapDefinition.TYPE_INTEGER) {
- elmsBuff.set(i,
Integer.valueOf((String) elmsBuff.get(i)));
- } else if (type ==
MultiHashMapDefinition.TYPE_BOOLEAN) {
- elmsBuff.set(i, new
Boolean((String) elmsBuff.get(i)));
- } else if (type ==
MultiHashMapDefinition.TYPE_FLOATING_POINT) {
- elmsBuff.set(i, new
Double((String) elmsBuff.get(i)));
- } else {
- // A string; do nothing.
- }
- }
-
- cyAttrs.setListAttribute(key,
attributeName, elmsBuff);
- } else { // Not a list.
- // Do the escaping thing.
-
- final StringBuilder elmBuff = new
StringBuilder();
- int inx2;
-
- for (inx2 = 0; inx2 < val.length();
inx2++) {
- char ch = val.charAt(inx2);
-
- if (ch == '\\') {
- if ((inx2 + 1) <
val.length()) {
- inx2++;
-
- char ch2 =
val.charAt(inx2);
-
- if (ch2 == 'n')
{
-
elmBuff.append('\n');
- } else if (ch2
== 't') {
-
elmBuff.append('\t');
- } else if (ch2
== 'b') {
-
elmBuff.append('\b');
- } else if (ch2
== 'r') {
-
elmBuff.append('\r');
- } else if (ch2
== 'f') {
-
elmBuff.append('\f');
- } else {
-
elmBuff.append(ch2);
- }
- } else {
- /* val ends in
'\' - just ignore it. */ }
- } else {
- elmBuff.append(ch);
- }
- }
-
- val = new String(elmBuff);
-
- if (firstLine) {
- if (type < 0) {
- while (true) {
- try {
-
Integer.valueOf(val);
- type =
MultiHashMapDefinition.TYPE_INTEGER;
-
- break;
- } catch
(Exception e) {
- }
-
- try {
- new
Double(val);
- type =
MultiHashMapDefinition.TYPE_FLOATING_POINT;
-
- break;
- } catch
(Exception e) {
- }
-
- //
try {
- //
new Boolean(val);
- //
type = MultiHashMapDefinition.TYPE_BOOLEAN;
- //
break; }
- //
catch (Exception e) {}
- type =
MultiHashMapDefinition.TYPE_STRING;
-
- break;
- }
- }
-
- firstLine = false;
- }
-
- if (type ==
MultiHashMapDefinition.TYPE_INTEGER) {
- cyAttrs.setAttribute(key,
attributeName, Integer.valueOf(val));
- } else if (type ==
MultiHashMapDefinition.TYPE_BOOLEAN) {
- cyAttrs.setAttribute(key,
attributeName, new Boolean(val));
- } else if (type ==
MultiHashMapDefinition.TYPE_FLOATING_POINT) {
- cyAttrs.setAttribute(key,
attributeName, new Double(val));
- } else {
- cyAttrs.setAttribute(key,
attributeName, val);
- }
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
-
- String message = "failed parsing attributes file at
line: " + lineNum
- + " with exception: ";
- throw new IOException(message + e.getMessage());
- }
- }
-}
Deleted:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java.asdf
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java.asdf
2012-05-07 22:10:30 UTC (rev 29139)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java.asdf
2012-05-07 22:19:00 UTC (rev 29140)
@@ -1,119 +0,0 @@
-package org.cytoscape.io.internal.read.datatable;
-
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-import java.util.HashMap;
-
-import org.cytoscape.io.internal.read.AbstractTableReader;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import static org.cytoscape.model.CyTableEntry.*;
-
-
-public class TextDataTableReader extends AbstractTableReader {
- @Tunable(description="Column delimiter character")
- public String delimiter = "\t";
-
- @Tunable(description="Table name")
- public String tableName = "";
-
- private String[] columnNames;
- private static final Logger logger =
LoggerFactory.getLogger(TextDataTableReader.class);
-
- public TextDataTableReader(InputStream inputStream, CyTableFactory
tableFactory) {
- super(inputStream, tableFactory);
- }
-
- @Override
- public void run(TaskMonitor tm) throws IOException {
- try {
-
-
- String line;
- final BufferedReader br = new BufferedReader(new
InputStreamReader(inputStream));
-
- line = br.readLine();
- final CyTable table = createTable(line);
-
- while ((line = br.readLine()) != null)
- processLine(table, line);
-
- cyTables = new CyTable[] { table };
-
- } finally {
- if (inputStream != null) {
- inputStream.close();
- inputStream = null;
- }
- }
-
- tm.setProgress(1.0);
- }
-
- @Override
- public void cancel() {
- }
-
- private CyTable createTable(String line) throws IOException {
- if (line == null)
- throw new IllegalStateException("Column names cannot be
null");
-
- columnNames = line.split(delimiter);
-
- checkForDuplicates( columnNames );
- final CyTable table = tableFactory.createTable(tableName,
columnNames[0],
- String.class,
true, true);
-
- for (String col : Arrays.copyOfRange(columnNames, 1,
columnNames.length))
- table.createColumn(col, String.class, false);
-
- return table;
- }
-
- private void checkForDuplicates(String[] names) throws IOException {
- Map<String,Integer> map = new HashMap<String,Integer>();
-
- for ( String n : names ) {
- if ( !map.containsKey(n) )
- map.put(n,0);
- map.put(n, map.get(n) + 1 );
- }
-
- if (map.keySet().size() != names.length) {
- String dupes = " ";
- for ( Map.Entry<String,Integer> entry : map.entrySet() )
- if ( entry.getValue() > 1 )
- dupes += entry.getKey() + " ";
-
- throw new IOException("Illegal duplicate column headers
found: " + dupes);
- }
- }
-
- private void processLine(CyTable table, String line) {
- String[] buffer = line.split(delimiter);
-
- if ( buffer.length != columnNames.length ) {
- logger.warn("Skipping line: '" + line + "' due to
incorrect length");
- return;
- }
-
- CyRow row = table.getRow(buffer[0]);
-
- for(int i = 0; i<buffer.length; i++)
- row.set(columnNames[i], buffer[i]);
- }
-}
Deleted:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory.java.asdf
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory.java.asdf
2012-05-07 22:10:30 UTC (rev 29139)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory.java.asdf
2012-05-07 22:19:00 UTC (rev 29140)
@@ -1,20 +0,0 @@
-package org.cytoscape.io.internal.read.datatable;
-
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.CyTableReader;
-import org.cytoscape.io.internal.read.AbstractTableReaderFactory;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.work.TaskIterator;
-
-
-public class TextDataTableReaderFactory extends AbstractTableReaderFactory {
- public TextDataTableReaderFactory(CyFileFilter filter, CyTableFactory
factory) {
- super(filter, factory);
- }
-
- public TaskIterator getTaskIterator() {
- return new TaskIterator(new TextDataTableReader(inputStream,
tableFactory));
- }
-}
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