diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java index 2230b02dcf80aa4cf9df1052f1bc008229afc17a..ffaef8cc4837764a7b89543dade09b387746d3f7 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;