Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 51be630..646a7f1 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -145,8 +145,8 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    int height = Platform.isAMac() ? 240 : 180;
-    Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, height);
+    Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, 
+               Platform.isAMacAndNotJS() ? 240 : 180);
   }
 
   private String getFrameTitle()
@@ -417,13 +417,17 @@ public class SequenceFetcher extends JPanel implements Runnable
     /*
      * tidy inputs and check there is something to search for
      */
-    String text = textArea.getText();
+    String t0 = textArea.getText();
+    String text = t0.trim();
     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
     {
       text = text.replace(",", ";");
     }
-    text = text.replaceAll("(\\s|[,; ])+", ";");
-    textArea.setText(text);
+    text = text.replaceAll("(\\s|[; ])+", ";");
+    if (!t0.equals(text)) 
+    {
+         textArea.setText(text);
+    }
     if (text.isEmpty())
     {
       // todo i18n
@@ -462,9 +466,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     List<DbSourceProxy> sources = sfetch
             .getSourceProxy((String) database.getSelectedItem());
     Iterator<DbSourceProxy> proxies = sources.iterator();
-    String[] qries;
-    List<String> nextFetch = Arrays
-            .asList(qries = textArea.getText().split(";"));
+    String[] qries = textArea.getText().trim().split(";");
+    List<String> nextFetch = Arrays.asList(qries);
     Iterator<String> en = Arrays.asList(new String[0]).iterator();
     int nqueries = qries.length;
 
@@ -750,13 +753,14 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-      DBRefEntry dbr = new DBRefEntry();
-      dbr.setSource(proxy.getDbSource());
-      dbr.setVersion(null);
+       // BH 2019.01.25 dbr is never used.
+//      DBRefEntry dbr = new DBRefEntry();
+//      dbr.setSource(proxy.getDbSource());
+//      dbr.setVersion(null);
       String accId = proxy.getAccessionIdFromQuery(q);
-      dbr.setAccessionId(accId);
+//      dbr.setAccessionId(accId);
       boolean rfound = false;
-      for (int r = 0; r < rs.length; r++)
+      for (int r = 0, nr = rs.length; r < nr; r++)
       {
         if (rs[r] != null)
         {