From 42c08ef2f5204439f7f6b11270b6cdfcdee3461f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 22 Mar 2007 10:12:25 +0000
Subject: [PATCH] fix
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5733 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/editor/FastaTextPane.java | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
index 2230b02dc..ffaef8cc4 100644
--- a/uk/ac/sanger/artemis/editor/FastaTextPane.java
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -62,7 +62,7 @@ public class FastaTextPane extends JScrollPane
private Vector listerners = new Vector();
private Vector threads = new Vector();
private static boolean remoteMfetch = false;
- public static HitInfo[] cacheHits = new HitInfo[100];
+ public static HitInfo[] cacheHits = new HitInfo[BigPane.CACHE_SIZE];
public static int nCacheHits = 0;
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(FastaTextPane.class);
@@ -628,6 +628,7 @@ public class FastaTextPane extends JScrollPane
{
final String env[] = { "PATH=/usr/local/pubseq/bin/:/nfs/disk100/pubseq/bin/" };
+ // split mfetch query up - max 70 hits per query
int nhits = hits.size()/70 + 1;
StringBuffer querySRS = new StringBuffer();
StringBuffer queryMfetch[] = new StringBuffer[nhits];
@@ -644,7 +645,8 @@ public class FastaTextPane extends JScrollPane
{
FileList fileList = new FileList();
FileAttributes attr = fileList.stat("/nfs/disk100/pubseq/bin/mfetch");
- remoteMfetch = attr.isFile();
+ if(attr != null)
+ remoteMfetch = attr.isFile();
}
Enumeration ehits = hits.elements();
@@ -657,7 +659,8 @@ public class FastaTextPane extends JScrollPane
HitInfo cacheHit = checkCache(hit);
if(cacheHit != null)
{
- logger4j.debug("Retrieved early from cache "+cacheHit.getID());
+ logger4j.debug("Retrieved early from cache "+cacheHit.getID()+
+ " cache size="+cacheHits.length);
hit.setOrganism(cacheHit.getOrganism());
hit.setDescription(cacheHit.getDescription());
hit.setGeneName(hit.getGeneName());
@@ -840,7 +843,8 @@ public class FastaTextPane extends JScrollPane
if(cacheHit != null && cacheHit.getEMBL() != null)
{
- logger4j.debug("Retrieved from cache "+cacheHit.getID());
+ logger4j.debug("Retrieved from cache "+cacheHit.getID()+
+ " cache size="+cacheHits.length);
hit.setEMBL(cacheHit.getEMBL());
hit.setEC_number(cacheHit.getEC_number());
continue;
--
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