X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=33d6d9289db1cef413e2448e581d2e50cf594768;hb=8a18973f7e4521c7dd3705ebd8fabd3ca08cfcaf;hp=29a0900aa4ed54d1b0d1590a0c668326a3cc1211;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 29a0900..33d6d92 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -33,23 +33,40 @@ import javax.swing.*;
 import javax.xml.namespace.QName;
 
 
-public class WSWUBlastClient {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
     CutAndPasteTransfer output = new CutAndPasteTransfer();
     int jobsRunning = 0;
 
-    public WSWUBlastClient(AlignmentI al, ArrayList ids) {
+    /**
+     * Creates a new WSWUBlastClient object.
+     *
+     * @param al DOCUMENT ME!
+     * @param ids DOCUMENT ME!
+     */
+    public WSWUBlastClient(AlignmentI al, ArrayList ids)
+    {
         output.setText(
             "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +
             "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
         Desktop.addInternalFrame(output,
             "BLASTing for unidentified sequences ", 800, 300);
 
-        for (int i = 0; i < ids.size(); i++) {
+        for (int i = 0; i < ids.size(); i++)
+        {
             SequenceI sequence = al.findName(ids.get(i).toString());
             StringBuffer nonGapped = new StringBuffer();
 
-            for (int n = 0; n < sequence.getSequence().length(); n++) {
-                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {
+            for (int n = 0; n < sequence.getSequence().length(); n++)
+            {
+                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
+                {
                     nonGapped.append(sequence.getCharAt(n));
                 }
             }
@@ -64,29 +81,41 @@ public class WSWUBlastClient {
         thread.start();
     }
 
-    void parseResult(String id1, String res) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id1 DOCUMENT ME!
+     * @param res DOCUMENT ME!
+     */
+    void parseResult(String id1, String res)
+    {
         StringTokenizer st = new StringTokenizer(res, "\n");
         String data;
         String id2;
         int maxFound = 90;
         StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");
 
-        while (st.hasMoreTokens()) {
+        while (st.hasMoreTokens())
+        {
             data = st.nextToken();
 
-            if (data.indexOf("database=\"uniprot\" id=") > -1) {
+            if (data.indexOf("database=\"uniprot\" id=") > -1)
+            {
                 int index = data.indexOf("database=\"uniprot\" id=") + 23;
                 id2 = data.substring(index, data.indexOf("\"", index));
 
-                while (data.indexOf("</alignment>") == -1) {
+                while (data.indexOf("</alignment>") == -1)
+                {
                     data = st.nextToken();
 
-                    if (data.indexOf("<identity>") > -1) {
+                    if (data.indexOf("<identity>") > -1)
+                    {
                         int value = Integer.parseInt(data.substring(data.indexOf(
                                         "<identity>") + 10,
                                     data.indexOf("</identity>")));
 
-                        if (value >= maxFound) {
+                        if (value >= maxFound)
+                        {
                             maxFound = value;
                             buffer.append(" " + id2 + " " + value + "%; ");
                         }
@@ -98,65 +127,81 @@ public class WSWUBlastClient {
         output.setText(output.getText() + buffer.toString());
     }
 
-    class ImageTwirler extends Thread {
+    class ImageTwirler extends Thread
+    {
         ImageIcon[] imageIcon;
         int imageIndex = 0;
 
-        public ImageTwirler() {
+        public ImageTwirler()
+        {
             imageIcon = new ImageIcon[9];
 
-            for (int i = 0; i < 9; i++) {
+            for (int i = 0; i < 9; i++)
+            {
                 java.net.URL url = getClass().getResource("/images/dna" +
                         (i + 1) + ".gif");
 
-                if (url != null) {
+                if (url != null)
+                {
                     imageIcon[i] = new ImageIcon(url);
                 }
             }
         }
 
-        public void run() {
-            while (jobsRunning > 0) {
-                try {
+        public void run()
+        {
+            while (jobsRunning > 0)
+            {
+                try
+                {
                     Thread.sleep(100);
                     imageIndex++;
                     imageIndex %= 9;
                     output.setFrameIcon(imageIcon[imageIndex]);
                     output.setTitle("BLASTing for unidentified sequences - " +
                         jobsRunning + " jobs running.");
-                } catch (Exception ex) {
+                }
+                catch (Exception ex)
+                {
                 }
             }
         }
     }
 
-    class BlastThread extends Thread {
+    class BlastThread extends Thread
+    {
         String sequence;
         String seqid;
         String jobid;
         boolean jobComplete = false;
 
-        BlastThread(String id, String sequence) {
+        BlastThread(String id, String sequence)
+        {
             this.sequence = sequence;
             seqid = id;
         }
 
-        public void run() {
+        public void run()
+        {
             StartJob();
 
-            while (!jobComplete) {
-                try {
+            while (!jobComplete)
+            {
+                try
+                {
                     Call call = (Call) new Service().createCall();
                     call.setTargetEndpointAddress(new java.net.URL(
                             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                     call.setOperationName(new QName("WSWUBlast", "polljob"));
 
-                    String result = (String) call.invoke(new Object[] {
+                    String result = (String) call.invoke(new Object[]
+                            {
                                 jobid, "xml"
                             });
 
                     if ((result.indexOf("JOB PENDING") == -1) &&
-                            (result.indexOf("JOB RUNNING") == -1)) {
+                            (result.indexOf("JOB RUNNING") == -1))
+                    {
                         parseResult(seqid, result);
                         jobComplete = true;
                         jobsRunning--;
@@ -165,12 +210,15 @@ public class WSWUBlastClient {
                     Thread.sleep(5000);
 
                     // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
-                } catch (Exception ex) {
+                }
+                catch (Exception ex)
+                {
                 }
             }
         }
 
-        void StartJob() {
+        void StartJob()
+        {
             HashMap params = new HashMap();
             params.put("database", "uniprot");
             params.put("sensitivity", "low");
@@ -183,20 +231,24 @@ public class WSWUBlastClient {
 
             byte[] seqbytes = sequence.getBytes();
 
-            try {
+            try
+            {
                 Call call = (Call) new Service().createCall();
                 call.setTargetEndpointAddress(new java.net.URL(
                         "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                 call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
 
-                String result = (String) call.invoke(new Object[] {
+                String result = (String) call.invoke(new Object[]
+                        {
                             params, seqbytes
                         });
                 jobid = result;
                 System.out.println(
                     "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +
                     jobid + "'");
-            } catch (Exception exp) {
+            }
+            catch (Exception exp)
+            {
                 System.err.println("WSWUBlastClient error:\n" + exp.toString());
                 exp.printStackTrace();
             }