diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
index 228529a1c81626ccd7cf84b3c1bdc3133dc8ea72..2230b02dcf80aa4cf9df1052f1bc008229afc17a 100644
--- a/uk/ac/sanger/artemis/editor/FastaTextPane.java
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -27,6 +27,9 @@ package uk.ac.sanger.artemis.editor;
import java.awt.Point;
import javax.swing.JTextArea;
import javax.swing.JScrollPane;
+
+import com.sshtools.j2ssh.sftp.FileAttributes;
+
import java.awt.Font;
import java.awt.Dimension;
import java.io.InputStream;
@@ -42,6 +45,7 @@ import java.util.StringTokenizer;
import java.net.URL;
import java.net.MalformedURLException;
+import uk.ac.sanger.artemis.components.filetree.FileList;
import uk.ac.sanger.artemis.util.WorkingGZIPInputStream;
public class FastaTextPane extends JScrollPane
@@ -57,7 +61,12 @@ public class FastaTextPane extends JScrollPane
private int qlen;
private Vector listerners = new Vector();
private Vector threads = new Vector();
-
+ private static boolean remoteMfetch = false;
+ public static HitInfo[] cacheHits = new HitInfo[100];
+ public static int nCacheHits = 0;
+ private static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(FastaTextPane.class);
+
public FastaTextPane(File dataFile)
{
super();
@@ -619,54 +628,113 @@ public class FastaTextPane extends JScrollPane
{
final String env[] = { "PATH=/usr/local/pubseq/bin/:/nfs/disk100/pubseq/bin/" };
- StringBuffer query = new StringBuffer();
-
+ int nhits = hits.size()/70 + 1;
+ StringBuffer querySRS = new StringBuffer();
+ StringBuffer queryMfetch[] = new StringBuffer[nhits];
+
int n = 0;
+ int this_nhit = 0;
+ nhits = 0;
File fmfetch = new File("/nfs/disk100/pubseq/bin/mfetch");
-
+
+
+ if(!fmfetch.exists() && !remoteMfetch &&
+ System.getProperty("j2ssh") != null &&
+ FileList.isConnected())
+ {
+ FileList fileList = new FileList();
+ FileAttributes attr = fileList.stat("/nfs/disk100/pubseq/bin/mfetch");
+ remoteMfetch = attr.isFile();
+ }
+
Enumeration ehits = hits.elements();
while(ehits.hasMoreElements() && keepRunning)
{
if(n>nretrieve)
break;
HitInfo hit = (HitInfo)ehits.nextElement();
+
+ HitInfo cacheHit = checkCache(hit);
+ if(cacheHit != null)
+ {
+ logger4j.debug("Retrieved early from cache "+cacheHit.getID());
+ hit.setOrganism(cacheHit.getOrganism());
+ hit.setDescription(cacheHit.getDescription());
+ hit.setGeneName(hit.getGeneName());
+ continue;
+ }
+
if(n > 0)
{
- query.append("|");
- if(fmfetch.exists())
- query.append("acc:");
+ querySRS.append("|");
+
+ if(nhits > 0)
+ queryMfetch[this_nhit].append("|acc:");
}
- query.append(hit.getAcc());
+ querySRS.append(hit.getAcc());
+
+ if(queryMfetch[this_nhit] == null)
+ queryMfetch[this_nhit] = new StringBuffer();
+
+ queryMfetch[this_nhit].append(hit.getAcc());
n++;
+ nhits++;
+ if(nhits > 70)
+ {
+ nhits = 0;
+ this_nhit++;
+ }
}
-
+
+ if(!keepRunning)
+ return;
+
BufferedReader strbuff = null;
File fgetz = new File("/usr/local/pubseq/bin/getz");
-
- if(fmfetch.exists())
+
+ if(fmfetch.exists() || remoteMfetch)
{
- String cmd[] = { "mfetch", "-f", "acc org des gen",
- "-d", "uniprot", "-i", "acc:"+query.toString() };
+ StringBuffer buff = new StringBuffer();
+ for(int i=0; i<queryMfetch.length; i++)
+ {
+ String mfetch = queryMfetch[i].toString();
+ if(mfetch.length() == 0)
+ continue;
+
+ if(fmfetch.exists()) // local
+ {
+ String cmd[] = { "mfetch", "-f", "acc org des gen",
+ "-d", "uniprot", "-i", "acc:"+mfetch };
- ExternalApplication app = new ExternalApplication(cmd,
- env,null);
- String res = app.getProcessStdout();
- //System.out.println(res);
- //System.out.println( app.getProcessStderr() );
- //for(int i=0; i<cmd.length; i++)
- // System.out.print(cmd[i]+" ");
-
- StringReader strread = new StringReader(res);
+ ExternalApplication app = new ExternalApplication(cmd,
+ env,null);
+ buff.append(app.getProcessStdout());
+ }
+ else // remote
+ {
+ String cmd =
+ "mfetch -f \"acc org des gen\" -d uniprot -i \"acc:"+mfetch+"\"" ;
+ uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
+ new uk.ac.sanger.artemis.j2ssh.SshPSUClient(cmd);
+ ssh.run();
+ buff.append(ssh.getStdOut());
+ }
+ }
+
+ StringReader strread = new StringReader(buff.toString());
strbuff = new BufferedReader(strread);
}
else if(!fgetz.exists())
{
try
{
- URL wgetz = new URL(DataCollectionPane.srs_url+
- "/wgetz?-f+acc%20org%20description%20gen+[uniprot-acc:"+
- query.toString()+"]+-lv+500");
+ String queryURL = DataCollectionPane.srs_url+
+ "/wgetz?-f+acc%20org%20description%20gen+[uniprot-acc:"+
+ querySRS.toString()+"]+-lv+500";
+ URL wgetz = new URL(queryURL);
+ logger4j.debug(queryURL);
+
InputStream in = wgetz.openStream();
strbuff = new BufferedReader(new InputStreamReader(in));
@@ -698,7 +766,7 @@ public class FastaTextPane extends JScrollPane
else
{
String cmd[] = { "getz", "-f", "acc org description gen",
- "[uniprot-acc:"+query.toString()+"]" };
+ "[uniprot-acc:"+querySRS.toString()+"]" };
ExternalApplication app = new ExternalApplication(cmd,
env,null);
@@ -729,7 +797,7 @@ public class FastaTextPane extends JScrollPane
if(hit == null)
{
- System.out.println("HIT NOT FOUND "+line);
+ logger4j.debug("HIT NOT FOUND "+line);
continue;
}
@@ -767,6 +835,17 @@ public class FastaTextPane extends JScrollPane
while(ehits.hasMoreElements() && keepRunning)
{
hit = (HitInfo)ehits.nextElement();
+
+ HitInfo cacheHit = checkCache(hit);
+
+ if(cacheHit != null && cacheHit.getEMBL() != null)
+ {
+ logger4j.debug("Retrieved from cache "+cacheHit.getID());
+ hit.setEMBL(cacheHit.getEMBL());
+ hit.setEC_number(cacheHit.getEC_number());
+ continue;
+ }
+
res = getUniprotLinkToDatabase(fgetz, fmfetch, hit, env, "embl");
int ind1 = res.indexOf("ID ");
@@ -791,12 +870,32 @@ public class FastaTextPane extends JScrollPane
StringTokenizer tok = new StringTokenizer(res);
tok.nextToken();
hit.setEC_number(tok.nextToken());
- }
+ }
+
+ if(nCacheHits >= cacheHits.length)
+ nCacheHits = 0;
+ cacheHits[nCacheHits] = hit;
+ nCacheHits++;
}
}
-
}
+ /**
+ *
+ * @param hit
+ * @return
+ */
+ private HitInfo checkCache(final HitInfo hit)
+ {
+ for(int i=0; i<cacheHits.length; i++)
+ {
+ if(cacheHits[i] != null &&
+ cacheHits[i].getID().equals(hit.getID()))
+ return cacheHits[i];
+ }
+ return null;
+ }
+
protected static String insertNewline(String s1, String s2)
{
int index = 0;
@@ -829,18 +928,25 @@ public class FastaTextPane extends JScrollPane
env,null);
res = app.getProcessStdout();
- //for(int i=0; i<cmd.length; i++)
- // System.out.print(cmd[i]+" ");
- //System.out.println("\n"+ app.getProcessStderr() );
- //System.out.println("\n"+res);
+ }
+ else if(remoteMfetch)
+ {
+ String cmd =
+ "mfetch -f id -d uniprot -i \"acc:"+hit.getID()+"\" -l "+DB ;
+ uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
+ new uk.ac.sanger.artemis.j2ssh.SshPSUClient(cmd);
+ ssh.run();
+ res = ssh.getStdOut();
}
else if(!fgetz.exists())
{
try
{
- URL wgetz = new URL(DataCollectionPane.srs_url+
- "/wgetz?-f+id+[uniprot-acc:"+hit.getAcc()+"]%3E"+DB);
-
+ final String queryURL = DataCollectionPane.srs_url+
+ "/wgetz?-f+id+[uniprot-acc:"+hit.getAcc()+"]%3E"+DB;
+ URL wgetz = new URL(queryURL);
+ logger4j.debug(queryURL);
+
InputStream in = wgetz.openStream();
BufferedReader strbuff = new BufferedReader(new InputStreamReader(in));
StringBuffer resBuff = new StringBuffer();