Author: mes
Date: 2012-01-27 18:08:32 -0800 (Fri, 27 Jan 2012)
New Revision: 28153
Added:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/MITABLine.java
Log:
initial checkin
Added:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/MITABLine.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/MITABLine.java
(rev 0)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/MITABLine.java
2012-01-28 02:08:32 UTC (rev 28153)
@@ -0,0 +1,287 @@
+package org.cytoscape.psi_mi.internal.plugin;
+
+import java.util.List;
+import java.util.ArrayList;
+
+// There are 15 tab separated columns. Columns can be further separated by
'|' and sub-columns
+// can be further separated by ':'
+// These are the columns
+//
+// 0 srcAlias:sourceRawId|srcAlias:srcAlias
+// 1 tgtAlias:targetRawId|tgtAlias:tgtAlias
+// 2 srcAlias:srcAlias|srcAlias:srcAlias
+// 3 tgtAlias:tgtAlias|tgtAlias:tgtAlias
+// 4 srcAlias:srcAlias|srcAlias:srcAlias
+// 5 tgtAlias:tgtAlias|tgtAlias:tgtAlias
+// 6 detectionMethod|detectionMethod
+// 7 authors|authors
+// 8 publicationIDKey:publicationIDValue|publicationIDKey:publicationIDValue
+// 9 srcAttrName:srcTaxonName|XXXX:XXXX
+// 10 tgtAttrName:tgtTaxonName|XXXX:XXXX
+// 11 interactionType|interactionType
+// 12 sourceDB|sourceDB
+// 13 interactionID|XXXX
+// 14 edgeScoreType:edgeScoreString|edgeScoreType:edgeScoreString
+
+public class MITABLine {
+
+ final char COLON = ':';
+ final char PIPE = '|';
+ final char TAB = ' ';
+
+ String sourceRawID = "";
+ String targetRawID = "";
+ String srcAttrName = "";
+ String srcTaxonName = "";
+ String tgtAttrName = "";
+ String tgtTaxonName = "";
+ String interactionID = "";
+
+ List<String> srcAliases = new ArrayList<String>(20);
+ List<String> tgtAliases = new ArrayList<String>(20);
+ List<String> authors = new ArrayList<String>(20);
+ List<String> detectionMethods = new ArrayList<String>(20);
+ List<String> publicationIDs = new ArrayList<String>(20);
+ List<String> publicationValues = new ArrayList<String>(20);
+ List<String> sourceDBs = new ArrayList<String>(20);
+ List<String> interactionTypes = new ArrayList<String>(20);
+ List<String> edgeScoreTypes = new ArrayList<String>(20);
+ List<String> edgeScoreStrings = new ArrayList<String>(20);
+
+ int colon = 0;
+ int tab = 0;
+ int pipe = 0;
+
+ private void init() {
+ sourceRawID = "";
+ targetRawID = "";
+ srcAttrName = "";
+ srcTaxonName = "";
+ tgtAttrName = "";
+ tgtTaxonName = "";
+ interactionID = "";
+ colon = 0;
+ tab = 0;
+ pipe = 0;
+ srcAliases.clear();
+ tgtAliases.clear();
+ authors.clear();
+ detectionMethods.clear();
+ publicationIDs.clear();
+ publicationValues.clear();
+ sourceDBs.clear();
+ interactionTypes.clear();
+ edgeScoreTypes.clear();
+ edgeScoreStrings.clear();
+ }
+
+ private int nextIndex(String s, int start) {
+ colon = s.indexOf(COLON, start);
+ pipe = s.indexOf(PIPE, start);
+ tab = s.indexOf(TAB, start);
+ return Math.min(colon, Math.min(pipe,tab));
+ }
+
+ void readLine(String line) {
+ init();
+
+ int begin = 0;
+ int end = 0;
+
+ // column 0
+ // get first source alias
+ end = nextIndex(line,0);
+ srcAliases.add(line.substring(begin,end));
+ begin = end+1;
+
+ // get sourceRawID
+ end = nextIndex(line,begin);
+ sourceRawID = line.substring(begin,end);
+ begin = end+1;
+
+ // get any additional source aliases
+ do {
+ end = nextIndex(line,begin);
+ srcAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 1
+ // get first target alias
+ end = nextIndex(line,begin);
+ tgtAliases.add(line.substring(begin,end));
+ begin = end+1;
+
+ // get targetRawID
+ end = nextIndex(line,begin);
+ targetRawID = line.substring(begin,end);
+ begin = end+1;
+
+ // get any additional target aliases
+ do {
+ end = nextIndex(line,begin);
+ tgtAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 2
+ // get any additional source aliases
+ do {
+ end = nextIndex(line,begin);
+ srcAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 3
+ // get any additional target aliases
+ do {
+ end = nextIndex(line,begin);
+ tgtAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 4
+ // get any additional source aliases
+ do {
+ end = nextIndex(line,begin);
+ srcAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 5
+ // get any additional target aliases
+ do {
+ end = nextIndex(line,begin);
+ tgtAliases.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 6
+ // get any detection methods
+ do {
+ end = nextIndex(line,begin);
+ detectionMethods.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 7
+ // get any authors
+ do {
+ end = nextIndex(line,begin);
+ authors.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 8
+ // get any additional publications
+ do {
+ end = nextIndex(line,begin);
+ publicationIDs.add(line.substring(begin,end));
+ begin = end+1;
+ end = nextIndex(line,begin);
+ publicationValues.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 9
+ // get source taxon
+ end = nextIndex(line,begin);
+ srcAttrName = line.substring(begin,end);
+ begin = end+1;
+
+ end = nextIndex(line,begin);
+ srcTaxonName = line.substring(begin,end);
+ begin = end+1;
+
+ // skip anything else in this column
+ do {
+ end = nextIndex(line,begin);
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 10
+ // get target taxon
+ end = nextIndex(line,begin);
+ tgtAttrName = line.substring(begin,end);
+ begin = end+1;
+
+ end = nextIndex(line,begin);
+ tgtTaxonName = line.substring(begin,end);
+ begin = end+1;
+
+ // skip anything else in this column
+ do {
+ end = nextIndex(line,begin);
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 11
+ // get any interaction types
+ do {
+ end = nextIndex(line,begin);
+ interactionTypes.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 12
+ // get any source databases
+ do {
+ end = nextIndex(line,begin);
+ sourceDBs.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 13
+ // get interaction ID
+ end = nextIndex(line,begin);
+ interactionID = line.substring(begin,end);
+ begin = end+1;
+
+ // skip anything else in this column
+ do {
+ end = nextIndex(line,begin);
+ begin = end+1;
+ } while ( end != tab );
+
+ // column 14
+ // get edge scores
+ do {
+ end = nextIndex(line,begin);
+ edgeScoreTypes.add(line.substring(begin,end));
+ begin = end+1;
+ end = nextIndex(line,begin);
+ edgeScoreStrings.add(line.substring(begin,end));
+ begin = end+1;
+ } while ( end != tab );
+ }
+
+ public void print() {
+ System.out.println("sourceRawID: " + sourceRawID);
+ System.out.println("targetRawID: " + targetRawID);
+ System.out.println("srcAttrName: " + srcAttrName);
+ System.out.println("srcTaxonName: " + srcTaxonName);
+ System.out.println("tgtAttrName: " + tgtAttrName);
+ System.out.println("tgtTaxonName: " + tgtTaxonName);
+ System.out.println("interactionID: " + interactionID);
+ printList("srcAliases", srcAliases);
+ printList("tgtAliases", tgtAliases);
+ printList("authors", authors);
+ printList("detectionMethods", detectionMethods);
+ printList("publicationIDs", publicationIDs);
+ printList("publicationValues", publicationValues);
+ printList("sourceDBs", sourceDBs);
+ printList("interactionTypes", interactionTypes);
+ printList("edgeScoreTypes", edgeScoreTypes);
+ printList("edgeScoreStrings", edgeScoreStrings);
+ System.out.println();
+ System.out.println();
+ }
+
+ private void printList(String name, List<String> vals) {
+ System.out.print(name + ": ");
+ for ( String s : vals )
+ System.out.print(s + ", ");
+ System.out.println();
+ }
+}
+
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