From b28c75ee284c48471485bb24031d859017e650a7 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 29 Sep 2004 15:54:49 +0000
Subject: [PATCH] add product line
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1895 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/editor/Annotation.java | 10 +++++++---
.../sanger/artemis/editor/DataCollectionPane.java | 6 ++++--
.../artemis/editor/DataViewInternalFrame.java | 15 ++++-----------
3 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/uk/ac/sanger/artemis/editor/Annotation.java b/uk/ac/sanger/artemis/editor/Annotation.java
index 90dc3c8c4..161e2ec9f 100644
--- a/uk/ac/sanger/artemis/editor/Annotation.java
+++ b/uk/ac/sanger/artemis/editor/Annotation.java
@@ -184,7 +184,7 @@ public class Annotation extends JEditorPane
s = getDatabaseHTML(s,"EMBL:");
s = getGeneDBHTML(s);
- int ind = s.indexOf("/gene");
+// int ind = s.indexOf("/gene");
Document doc = getDocument();
int offset = doc.getLength();
@@ -394,9 +394,13 @@ public class Annotation extends JEditorPane
ind1 = ind2+1;
}
- // if ortholog then delete gene line as well
+ // if ortholog then delete gene and product lines as well
if(ortholog)
- ind2 = txt.indexOf("<br>",ind2+4);
+ {
+ ind2 = txt.indexOf("<br>/product=");
+ if(ind2 > -1)
+ ind2 = txt.indexOf("<br>",ind2+4);
+ }
if(ind2 == -1 || ind2 > txt.length())
ind2 = txt.length();
diff --git a/uk/ac/sanger/artemis/editor/DataCollectionPane.java b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
index c48bcd753..d5855547a 100644
--- a/uk/ac/sanger/artemis/editor/DataCollectionPane.java
+++ b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
@@ -468,7 +468,6 @@ public class DataCollectionPane extends JScrollPane
{
public Object construct()
{
-
final String env[] = { "PATH=/usr/local/pubseq/bin/" };
StringBuffer query = new StringBuffer();
@@ -841,7 +840,10 @@ public class DataCollectionPane extends JScrollPane
{
String geneName = hit.getGeneName();
if(hit.getGeneName() != null)
- orthoText = "<br>\n/gene=\""+hit.getGeneName()+"\"";
+ orthoText = "<br>\n/gene=\""+hit.getGeneName()+"\""+
+ "<br>\n/product=\""+hit.getDescription()+"\"";
+ else
+ orthoText = "<br>\n/product=\""+hit.getDescription()+"\"";
}
// System.out.println("ID "+hit.getID());
diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
index 366c7abee..d458e60fa 100644
--- a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
+++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
@@ -208,21 +208,14 @@ public class DataViewInternalFrame extends JInternalFrame
protected void reReadSelectedResults()
{
- JSplitPane split = (JSplitPane)tabPane.getSelectedComponent();
+ ActiveJSplitPane split = (ActiveJSplitPane)tabPane.getSelectedComponent();
Component comps[] = split.getComponents();
for(int i=0; i<comps.length;i++)
{
- if(comps[i] instanceof JSplitPane)
+ if(comps[i] instanceof FastaTextPane)
{
- Component comps2[] = ((JSplitPane)comps[i]).getComponents();
- for(int j=0; j<comps2.length;j++)
- {
- if(comps2[j] instanceof FastaTextPane)
- {
- ((FastaTextPane)comps2[j]).reRead();
- return;
- }
- }
+ ((FastaTextPane)comps[i]).reRead();
+ return;
}
}
}
--
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