From d18d71f7fd61e73eb89fc10b9a4c2b8d83f6c59c Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 30 Jul 2007 08:54:01 +0000
Subject: [PATCH] updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6259 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../genebuilder/ortholog/MatchPanel.java | 39 +++++++++++--------
.../genebuilder/ortholog/OrthologTable.java | 29 ++++++++++++--
2 files changed, 47 insertions(+), 21 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
index 148916aec..54cb2e54e 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
@@ -17,7 +17,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java,v 1.10 2007-07-24 08:41:12 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java,v 1.11 2007-07-30 08:54:01 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder.ortholog;
@@ -61,7 +61,11 @@ public class MatchPanel extends JPanel
private Vector editableComponents;
private JButton hide_show_ortho;
private JButton hide_show_sim;
-
+ private static String ORTHOLOG = "orthologous_to";
+ private static String PARALOG = "paralogous_to";
+ private static String SIMILARITY = "similarity";
+ private static String[] SO_CLUSTER_NAMES =
+ { ORTHOLOG, PARALOG, SIMILARITY };
public MatchPanel(final Feature feature)
{
@@ -85,23 +89,21 @@ public class MatchPanel extends JPanel
* @param qualifierName
* @return
*/
- public boolean isMatchTag(String qualifierName)
+ public static boolean isMatchTag(final String qualifierName)
{
- if(qualifierName.startsWith("/"))
- qualifierName = qualifierName.substring(1);
-
- if(qualifierName.startsWith("ortholog") ||
- qualifierName.startsWith("similarity"))
- return true;
+ for(int i=0; i<SO_CLUSTER_NAMES.length;i++)
+ if(qualifierName.equals(SO_CLUSTER_NAMES[i]) ||
+ qualifierName.equals(SO_CLUSTER_NAMES[i]+"="))
+ return true;
return false;
}
private Component createMatchQualifiersComponent(final Feature feature)
{
editableComponents = new Vector();
- final Qualifier orthoQualifier = matchQualifiers.getQualifierByName("ortholog");
- final Qualifier paraQualifier = matchQualifiers.getQualifierByName("paralog");
- final Qualifier simQualifier = matchQualifiers.getQualifierByName("similarity");
+ final Qualifier orthoQualifier = matchQualifiers.getQualifierByName(ORTHOLOG);
+ final Qualifier paraQualifier = matchQualifiers.getQualifierByName(PARALOG);
+ final Qualifier simQualifier = matchQualifiers.getQualifierByName(SIMILARITY);
if(databases == null)
{
@@ -133,7 +135,7 @@ public class MatchPanel extends JPanel
if(select == JOptionPane.CANCEL_OPTION)
return;
- add("ortholog", ((String)dbs.getSelectedItem())+":"+
+ add(ORTHOLOG, ((String)dbs.getSelectedItem())+":"+
accession.getText().trim(), feature);
}
});
@@ -146,8 +148,11 @@ public class MatchPanel extends JPanel
///
/// temp
///
- //if(orthoQualifier != null)
- //{
+ if(orthoQualifier != null)
+ {
+ if(orthoQualifier instanceof QualifierLazyLoading)
+ ((QualifierLazyLoading)orthoQualifier).setForceLoad(true);
+ }
if(hide_show_ortho == null)
hide_show_ortho = new JButton("-");
@@ -185,7 +190,7 @@ public class MatchPanel extends JPanel
if(select == JOptionPane.CANCEL_OPTION)
return;
- add("paralog", ((String)dbs.getSelectedItem())+":"+
+ add(PARALOG, ((String)dbs.getSelectedItem())+":"+
accession.getText().trim(), feature);
}
});
@@ -225,7 +230,7 @@ public class MatchPanel extends JPanel
if(select == JOptionPane.CANCEL_OPTION)
return;
- add("similarity", accession.getText().trim(), feature);
+ add(SIMILARITY, accession.getText().trim(), feature);
}
});
xBox = Box.createHorizontalBox();
diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
index 8f2ca093a..99c9b71a3 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
@@ -54,10 +54,11 @@ import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.StringVector;
public class OrthologTable extends AbstractMatchTable
{
- private int NUMBER_COLUMNS = 3;
+ private static int NUMBER_COLUMNS = 3;
private Vector rowData = new Vector();
private Vector tableData = new Vector(NUMBER_COLUMNS);
private JTable orthologTable;
@@ -66,7 +67,6 @@ public class OrthologTable extends AbstractMatchTable
//
// column headings
- final static String ORGANISM_COL = "Organism";
final static String ORTHO_COL = "Ortholog";
final static String DESCRIPTION_COL = "Description";
final static String REMOVE_BUTTON_COL = "";
@@ -92,6 +92,23 @@ public class OrthologTable extends AbstractMatchTable
tableData.setElementAt(REMOVE_BUTTON_COL,2);
// add row data
+ if(origQualifier != null)
+ {
+ int columnIndex;
+ StringVector values = origQualifier.getValues();
+ for(int i=0; i<values.size(); i++)
+ {
+ StringVector rowStr = StringVector.getStrings((String)values.get(i), ";");
+ Vector thisRowData = new Vector(NUMBER_COLUMNS);
+ thisRowData.setSize(NUMBER_COLUMNS);
+
+ columnIndex = tableData.indexOf(ORTHO_COL);
+ thisRowData.setElementAt((String)rowStr.get(0), columnIndex);
+ columnIndex = tableData.indexOf(DESCRIPTION_COL);
+ thisRowData.setElementAt("blah", columnIndex);
+ rowData.add(thisRowData);
+ }
+ }
Vector thisRowData = new Vector();
thisRowData.add("Bpseudomallei:BPSL0003");
thisRowData.add("blah blah");
@@ -236,8 +253,12 @@ public class OrthologTable extends AbstractMatchTable
*/
protected String updateQualifierString(int row)
{
- // TODO Auto-generated method stub
- return null;
+ StringBuffer orthologStr = new StringBuffer(
+ (String)getTable().getValueAt(row, getColumnIndex(ORTHO_COL)) ); // ortholog link
+ orthologStr.append(";");
+ orthologStr.append(
+ (String)getTable().getValueAt(row, getColumnIndex(DESCRIPTION_COL)) ); // description
+ return orthologStr.toString();
}
--
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