X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=a3604d67c0b93dcc3ee618dde69e563f4584ceb2;hb=c7633fc4fc9799d9a906c8b60b3e3981a2c0b4fb;hp=2799a7e2921d5867352c63a98e0fe635b57ce2d7;hpb=b2cedc8371f6624859f107581e6d84e841d4114b;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2799a7e..a3604d6 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -79,6 +79,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
@@ -90,6 +91,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
+import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.DataInputStream;
@@ -116,7 +118,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
-import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
@@ -1194,17 +1195,17 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector settingsAdded = new Vector();
+        Vector<String> settingsAdded = new Vector<String>();
         Object gstyle = null;
         GraduatedColor gcol = null;
         if (renderOrder != null)
         {
-          for (int ro = 0; ro < renderOrder.length; ro++)
+          for (String featureType : renderOrder)
           {
             gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                    .getFeatureStyle(renderOrder[ro]);
+                    .getFeatureStyle(featureType);
             Setting setting = new Setting();
-            setting.setType(renderOrder[ro]);
+            setting.setType(featureType);
             if (gstyle instanceof GraduatedColor)
             {
               gcol = (GraduatedColor) gstyle;
@@ -1219,57 +1220,30 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.getSeqPanel().seqCanvas
-                      .getFeatureRenderer().getColour(renderOrder[ro])
-                      .getRGB());
+              setting.setColour(((Color) gstyle).getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
-                    renderOrder[ro]));
+                    featureType));
             float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                    .getOrder(renderOrder[ro]);
+                    .getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
             }
             fs.addSetting(setting);
-            settingsAdded.addElement(renderOrder[ro]);
+            settingsAdded.addElement(featureType);
           }
         }
 
-        // Make sure we save none displayed feature settings
-        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                .getFeatureColours().keySet().iterator();
-        while (en.hasNext())
-        {
-          String key = en.next().toString();
-          if (settingsAdded.contains(key))
-          {
-            continue;
-          }
-
-          Setting setting = new Setting();
-          setting.setType(key);
-          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getColour(key).getRGB());
-
-          setting.setDisplay(false);
-          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getOrder(key);
-          if (rorder > -1)
-          {
-            setting.setOrder(rorder);
-          }
-          fs.addSetting(setting);
-          settingsAdded.addElement(key);
-        }
         // is groups actually supposed to be a map here ?
-        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+        Iterator<String> en = ap.getSeqPanel().seqCanvas
+                .getFeatureRenderer()
                 .getFeatureGroups().iterator();
-        Vector groupsAdded = new Vector();
+        Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
-          String grp = en.next().toString();
+          String grp = en.next();
           if (groupsAdded.contains(grp))
           {
             continue;
@@ -4047,18 +4021,22 @@ public class Jalview2XML
   }
 
   /**
+   * Answers true if 'version' is equal to or later than 'supported', where each
+   * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+   * changes. Development and test values for 'version' are leniently treated
+   * i.e. answer true.
    * 
    * @param supported
    *          - minimum version we are comparing against
    * @param version
-   *          - version of data being processsed.
-   * @return true if version is development/null or evaluates to the same or
-   *         later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+   *          - version of data being processsed
+   * @return
    */
   public static boolean isVersionStringLaterThan(String supported,
           String version)
   {
-    if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+    if (supported == null || version == null
+            || version.equalsIgnoreCase("DEVELOPMENT BUILD")
             || version.equalsIgnoreCase("Test")
             || version.equalsIgnoreCase("AUTOMATED BUILD"))
     {
@@ -4069,45 +4047,8 @@ public class Jalview2XML
     }
     else
     {
-      StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
-              version, ".");
-      while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
-      {
-        // convert b to decimal to catch bugfix releases within a series
-        String curT = currentV.nextToken().toLowerCase().replace('b', '.');
-        String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
-        try
-        {
-          float supportedVersionToken = Float.parseFloat(curT);
-          float myVersiontoken = Float.parseFloat(fileT);
-          if (supportedVersionToken > myVersiontoken)
-          {
-            // current version is newer than the version that wrote the file
-            return false;
-          }
-          if (supportedVersionToken < myVersiontoken)
-          {
-            // current version is older than the version that wrote the file
-            return true;
-          }
-        } catch (NumberFormatException nfe)
-        {
-          System.err
-                  .println("** WARNING: Version comparison failed for tokens ("
-                          + curT
-                          + ") and ("
-                          + fileT
-                          + ")\n** Current: '"
-                          + supported + "' and Version: '" + version + "'");
-        }
-      }
-      if (currentV.hasMoreElements())
-      {
-        // fileV has no minor version but identical series to current
-        return false;
-      }
+      return StringUtils.compareVersions(version, supported, "b") >= 0;
     }
-    return true;
   }
 
   Vector<JalviewStructureDisplayI> newStructureViewers = null;