JAL-3633 ensure check both http:// or https:// for urls

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1e292ba..eaa5fa8 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,28 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -79,6 +57,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -451,10 +430,8 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      
-
       protocol = AppletFormatAdapter.checkProtocol(file);
-      
+
       if (protocol == DataSourceType.FILE)
       {
         if (!(new File(file)).exists())
@@ -650,11 +627,14 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-          FileFormatI outFormat=null;
-          try {
+          FileFormatI outFormat = null;
+          try
+          {
             outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP) {
-            System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+          } catch (Exception formatP)
+          {
+            System.out.println("Couldn't parse " + outFormat
+                    + " as a valid Jalview format string.");
           }
           if (outFormat != null)
           {
@@ -698,8 +678,8 @@ public class Jalview
               jalview.bin.Cache.getDefault("www.jalview.org",
                       "https://www.jalview.org")
                       + "/examples/exampleFile_2_7.jvp");
-      if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+              || file.equals(
                       "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
         file.replace("http:", "https:");

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4be7d0e..b1efed6 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -138,6 +138,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
@@ -1037,7 +1038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
@@ -1047,7 +1048,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
@@ -1094,7 +1095,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null || (currentFileFormat == null)
-            || fileName.startsWith("http"))
+            || HttpUtils.startsWithHttpOrHttps(fileName))
     {
       saveAs_actionPerformed(null);
     }
@@ -1749,7 +1750,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode 
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+   * or the sequence under cursor in keyboard mode
    * 
    * @param up
    *          or down (if !up)
@@ -1760,23 +1762,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      if (viewport.cursorMode) 
+      if (viewport.cursorMode)
       {
         sg = new SequenceGroup();
-        sg.addSequence(viewport.getAlignment()
-                .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
-      } else {
+        sg.addSequence(viewport.getAlignment().getSequenceAt(
+                alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+      }
+      else
+      {
         return;
       }
     }
-    
+
     if (sg.getSize() < 1)
     {
-        return;
+      return;
     }
-    
+
     // TODO: JAL-3733 - add an event to the undo buffer for this !
-    
+
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ca0423b..0e062ac 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -24,6 +24,54 @@ import static jalview.math.RotatableMatrix.Axis.X;
 import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
 import jalview.analysis.Conservation;
 import jalview.analysis.PCA;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -85,6 +133,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.Format;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
@@ -150,54 +199,6 @@ import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
 import jalview.xml.binding.jalview.ThresholdType;
 import jalview.xml.binding.jalview.VAMSAS;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.SwingUtilities;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.Marshaller;
-import javax.xml.datatype.DatatypeConfigurationException;
-import javax.xml.datatype.DatatypeFactory;
-import javax.xml.datatype.XMLGregorianCalendar;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamReader;
-
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
  * 
@@ -946,7 +947,7 @@ public class Jalview2XML
         else
         {
           vamsasSeq = createVamsasSequence(id, jds);
-//          vamsasSet.addSequence(vamsasSeq);
+          // vamsasSet.addSequence(vamsasSeq);
           vamsasSet.getSequence().add(vamsasSeq);
           vamsasSetIds.put(id, vamsasSeq);
           seqRefIds.put(id, jds);
@@ -1339,9 +1340,8 @@ public class Jalview2XML
 
             if (colourScheme instanceof jalview.schemes.UserColourScheme)
             {
-              jGroup.setColour(
-                      setUserColourScheme(colourScheme, userColours,
-                              object));
+              jGroup.setColour(setUserColourScheme(colourScheme,
+                      userColours, object));
             }
             else
             {
@@ -1387,7 +1387,7 @@ public class Jalview2XML
         }
       }
 
-      //jms.setJGroup(groups);
+      // jms.setJGroup(groups);
       Object group;
       for (JGroup grp : groups)
       {
@@ -1524,11 +1524,13 @@ public class Jalview2XML
              * save any filter for the feature type
              */
             FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
-            if (filter != null)  {
-              Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+            if (filter != null)
+            {
+              Iterator<FeatureMatcherI> filters = filter.getMatchers()
+                      .iterator();
               FeatureMatcherI firstFilter = filters.next();
-              setting.setMatcherSet(Jalview2XML.marshalFilter(
-                      firstFilter, filters, filter.isAnded()));
+              setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+                      filters, filter.isAnded()));
             }
 
             /*
@@ -1577,8 +1579,7 @@ public class Jalview2XML
 
             setting.setDisplay(
                     av.getFeaturesDisplayed().isVisible(featureType));
-            float rorder = fr
-                    .getOrder(featureType);
+            float rorder = fr.getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
@@ -1602,7 +1603,7 @@ public class Jalview2XML
           Group g = new Group();
           g.setName(grp);
           g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
-                          .booleanValue());
+                  .booleanValue());
           // fs.addGroup(g);
           fs.getGroup().add(g);
           groupsAdded.addElement(grp);
@@ -2368,7 +2369,8 @@ public class Jalview2XML
   {
     if (calcIdParam.getVersion().equals("1.0"))
     {
-      final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+      final String[] calcIds = calcIdParam.getServiceURL()
+              .toArray(new String[0]);
       Jws2Instance service = Jws2Discoverer.getDiscoverer()
               .getPreferredServiceFor(calcIds);
       if (service != null)
@@ -2654,12 +2656,12 @@ public class Jalview2XML
     return id;
   }
 
-  jalview.schemes.UserColourScheme getUserColourScheme(
-          JalviewModel jm, String id)
+  jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+          String id)
   {
     List<UserColours> uc = jm.getUserColours();
     UserColours colours = null;
-/*
+    /*
     for (int i = 0; i < uc.length; i++)
     {
       if (uc[i].getId().equals(id))
@@ -2668,7 +2670,7 @@ public class Jalview2XML
         break;
       }
     }
-*/
+    */
     for (UserColours c : uc)
     {
       if (c.getId().equals(id))
@@ -2696,10 +2698,9 @@ public class Jalview2XML
       newColours = new java.awt.Color[23];
       for (int i = 0; i < 23; i++)
       {
-        newColours[i] = new java.awt.Color(Integer.parseInt(
-                colours.getUserColourScheme().getColour().get(i + 24)
-                        .getRGB(),
-                16));
+        newColours[i] = new java.awt.Color(
+                Integer.parseInt(colours.getUserColourScheme().getColour()
+                        .get(i + 24).getRGB(), 16));
       }
       ucs.setLowerCaseColours(newColours);
     }
@@ -2778,7 +2779,7 @@ public class Jalview2XML
     viewportsAdded.clear();
     frefedSequence = null;
 
-    if (file.startsWith("http://"))
+    if (HttpUtils.startsWithHttpOrHttps(file))
     {
       url = new URL(file);
     }
@@ -2855,8 +2856,8 @@ public class Jalview2XML
           XMLStreamReader streamReader = XMLInputFactory.newInstance()
                   .createXMLStreamReader(jin);
           javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-          JAXBElement<JalviewModel> jbe = um
-                  .unmarshal(streamReader, JalviewModel.class);
+          JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
+                  JalviewModel.class);
           JalviewModel object = jbe.getValue();
 
           /*
@@ -3276,7 +3277,8 @@ public class Jalview2XML
   AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
   {
-    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+            .get(0);
     List<Sequence> vamsasSeqs = vamsasSet.getSequence();
 
     // JalviewModelSequence jms = object.getJalviewModelSequence();
@@ -3335,11 +3337,10 @@ public class Jalview2XML
           if (tmpSeq.getStart() != jseq.getStart()
                   || tmpSeq.getEnd() != jseq.getEnd())
           {
-            System.err.println(
-                    String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
-                            tmpSeq.getName(), tmpSeq.getStart(),
-                            tmpSeq.getEnd(), jseq.getStart(),
-                            jseq.getEnd()));
+            System.err.println(String.format(
+                    "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+                    tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+                    jseq.getStart(), jseq.getEnd()));
           }
         }
         else
@@ -3622,8 +3623,8 @@ public class Jalview2XML
               else
               {
                 // defer to later
-                frefedSequence.add(
-                        newAlcodMapRef(map.getDnasq(), cf, mapping));
+                frefedSequence
+                        .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
               }
             }
           }
@@ -3831,8 +3832,7 @@ public class Jalview2XML
         jaa.setCalcId(annotation.getCalcId());
         if (annotation.getProperty().size() > 0)
         {
-          for (Annotation.Property prop : annotation
-                  .getProperty())
+          for (Annotation.Property prop : annotation.getProperty())
           {
             jaa.setProperty(prop.getName(), prop.getValue());
           }
@@ -3913,9 +3913,9 @@ public class Jalview2XML
         sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
         sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
         // attributes with a default in the schema are never null
-          sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
-          sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
-          sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+        sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+        sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+        sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
         sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
         if (jGroup.getConsThreshold() != null
                 && jGroup.getConsThreshold().intValue() != 0)
@@ -3959,8 +3959,9 @@ public class Jalview2XML
         if (addAnnotSchemeGroup)
         {
           // reconstruct the annotation colourscheme
-          sg.setColourScheme(constructAnnotationColour(
-                  jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+          sg.setColourScheme(
+                  constructAnnotationColour(jGroup.getAnnotationColours(),
+                          null, al, jalviewModel, false));
         }
       }
     }
@@ -4166,8 +4167,8 @@ public class Jalview2XML
    * @param av
    * @param ap
    */
-  protected void loadTrees(JalviewModel jm, Viewport view,
-          AlignFrame af, AlignViewport av, AlignmentPanel ap)
+  protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+          AlignViewport av, AlignmentPanel ap)
   {
     // TODO result of automated refactoring - are all these parameters needed?
     try
@@ -4275,8 +4276,8 @@ public class Jalview2XML
           for (int s = 0; s < structureStateCount; s++)
           {
             // check to see if we haven't already created this structure view
-            final StructureState structureState = pdbid
-                    .getStructureState().get(s);
+            final StructureState structureState = pdbid.getStructureState()
+                    .get(s);
             String sviewid = (structureState.getViewId() == null) ? null
                     : structureState.getViewId() + uniqueSetSuffix;
             jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
@@ -4339,8 +4340,8 @@ public class Jalview2XML
             colourByViewer &= structureState.isColourByJmol();
             jmoldat.setColourByViewer(colourByViewer);
 
-            if (jmoldat.getStateData().length() < structureState
-                    .getValue()/*Content()*/.length())
+            if (jmoldat.getStateData().length() < structureState.getValue()
+                    /*Content()*/.length())
             {
               jmoldat.setStateData(structureState.getValue());// Content());
             }
@@ -4535,7 +4536,8 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
+        newFileLoc
+                .append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -4848,9 +4850,9 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, List<JSeq> JSEQ,
-          List<SequenceI> hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List<JvAnnotRow> autoAlan)
+          List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List<JvAnnotRow> autoAlan)
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
@@ -4931,9 +4933,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -5009,9 +5010,8 @@ public class Jalview2XML
     af.changeColour(cs);
     viewport.setColourAppliesToAllGroups(true);
 
-    viewport
-            .setShowSequenceFeatures(
-                    safeBoolean(view.isShowSequenceFeatures()));
+    viewport.setShowSequenceFeatures(
+            safeBoolean(view.isShowSequenceFeatures()));
 
     viewport.setCentreColumnLabels(view.isCentreColumnLabels());
     viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
@@ -5035,13 +5035,13 @@ public class Jalview2XML
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
-      String[] renderOrder = new String[jm.getFeatureSettings()
-              .getSetting().size()];
+      String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+              .size()];
       Map<String, FeatureColourI> featureColours = new Hashtable<>();
       Map<String, Float> featureOrder = new Hashtable<>();
 
-      for (int fs = 0; fs < jm.getFeatureSettings()
-              .getSetting().size(); fs++)
+      for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+              .size(); fs++)
       {
         Setting setting = jm.getFeatureSettings().getSetting().get(fs);
         String featureType = setting.getType();
@@ -5053,8 +5053,8 @@ public class Jalview2XML
                 .getMatcherSet();
         if (filters != null)
         {
-          FeatureMatcherSetI filter = Jalview2XML
-                  .parseFilter(featureType, filters);
+          FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+                  filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5086,8 +5086,7 @@ public class Jalview2XML
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
           FeatureColourI gc = new FeatureColour(maxColour, minColour,
-                  maxColour,
-                  noValueColour, min, max);
+                  maxColour, noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
             gc.setAttributeName(setting.getAttributeName().toArray(
@@ -5121,8 +5120,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5595,6 +5593,7 @@ public class Jalview2XML
       }
     }
   }
+
   /**
    * 
    * @param vamsasSeq
@@ -6341,8 +6340,8 @@ public class Jalview2XML
    * @param fcol
    * @return
    */
-  public static Colour marshalColour(
-          String featureType, FeatureColourI fcol)
+  public static Colour marshalColour(String featureType,
+          FeatureColourI fcol)
   {
     Colour col = new Colour();
     if (fcol.isSimpleColour())
@@ -6403,7 +6402,7 @@ public class Jalview2XML
           boolean and)
   {
     jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-  
+
     if (filters.hasNext())
     {
       /*
@@ -6453,7 +6452,7 @@ public class Jalview2XML
       }
       result.setMatchCondition(matcherModel);
     }
-  
+
     return result;
   }
 
@@ -6464,8 +6463,7 @@ public class Jalview2XML
    * @param matcherSetModel
    * @return
    */
-  public static FeatureMatcherSetI parseFilter(
-          String featureType,
+  public static FeatureMatcherSetI parseFilter(String featureType,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
   {
     FeatureMatcherSetI result = new FeatureMatcherSet();
@@ -6480,7 +6478,7 @@ public class Jalview2XML
                       featureType, e.getMessage()));
       // return as much as was parsed up to the error
     }
-  
+
     return result;
   }
 
@@ -6495,8 +6493,7 @@ public class Jalview2XML
    * @throws IllegalStateException
    *           if AND and OR conditions are mixed
    */
-  protected static void parseFilterConditions(
-          FeatureMatcherSetI matcherSet,
+  protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
           boolean and)
   {
@@ -6518,7 +6515,7 @@ public class Jalview2XML
       else if (filterBy == FilterBy.BY_SCORE)
       {
         matchCondition = FeatureMatcher.byScore(cond, pattern);
-  
+
       }
       else if (filterBy == FilterBy.BY_ATTRIBUTE)
       {
@@ -6528,7 +6525,7 @@ public class Jalview2XML
         matchCondition = FeatureMatcher.byAttribute(cond, pattern,
                 attNames);
       }
-  
+
       /*
        * note this throws IllegalStateException if AND-ing to a 
        * previously OR-ed compound condition, or vice versa
@@ -6571,13 +6568,13 @@ public class Jalview2XML
   public static FeatureColourI parseColour(Colour colourModel)
   {
     FeatureColourI colour = null;
-  
+
     if (colourModel.getMax() != null)
     {
       Color mincol = null;
       Color maxcol = null;
       Color noValueColour = null;
-  
+
       try
       {
         mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
@@ -6586,7 +6583,7 @@ public class Jalview2XML
       {
         Cache.log.warn("Couldn't parse out graduated feature color.", e);
       }
-  
+
       NoValueColour noCol = colourModel.getNoValueColour();
       if (noCol == NoValueColour.MIN)
       {
@@ -6596,7 +6593,7 @@ public class Jalview2XML
       {
         noValueColour = maxcol;
       }
-  
+
       colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
@@ -6635,7 +6632,7 @@ public class Jalview2XML
       Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
       colour = new FeatureColour(color);
     }
-  
+
     return colour;
   }
 }

diff --git a/src/jalview/util/HttpUtils.java b/src/jalview/util/HttpUtils.java
index a5a9460..74f77a2 100644 (file)
--- a/src/jalview/util/HttpUtils.java
+++ b/src/jalview/util/HttpUtils.java
@@ -64,4 +64,9 @@ public class HttpUtils
     return false;
   }
 
+  public static boolean startsWithHttpOrHttps(String file)
+  {
+    return file.startsWith("http://") || file.startsWith("https://");
+  }
+
 }