JAL-3253/JAL-3258 FileLoader fix for use of file.separator

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 09f8de7..ee97b7f 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -708,7 +708,7 @@ public class Cache
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);
-      if (andSave && !propsAreReadOnly)
+      if (andSave && !propsAreReadOnly && propertiesFile != null)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d51da33..1fb45bc 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -890,7 +890,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
     StringBuilder out = new StringBuilder(256);
 
-    out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
+    out.append(String.format("%s %d" + newline, GFF_VERSION,
+            gffVersion == 0 ? 2 : gffVersion));
 
     if (!includeNonPositionalFeatures
             && (visibleColours == null || visibleColours.isEmpty()))

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0d46e76..38594df 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -361,9 +361,9 @@ public class FileLoader implements Runnable
             if (downloadStructureFile)
             {
               String structExt = format.getExtensions().split(",")[0];
-              String urlLeafName = file.substring(
-                      file.lastIndexOf(
-                              System.getProperty("file.separator")),
+              int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+                      : System.getProperty("file.separator"));
+              String urlLeafName = file.substring(pt,
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index fdef53d..a56a0de 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -491,7 +491,9 @@ public class FeaturesFileTest
             + "ENDGROUP\tuniprot\n\n"
             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
@@ -506,7 +508,7 @@ public class FeaturesFileTest
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "ENDGROUP\tuniprot\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * now set Pfam visible
@@ -528,7 +530,7 @@ public class FeaturesFileTest
             // null / empty group features are output after named groups
             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * hide uniprot group
@@ -540,7 +542,7 @@ public class FeaturesFileTest
             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
             false);
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * include non-positional (overrides group not shown)
@@ -556,7 +558,7 @@ public class FeaturesFileTest
             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 
   @Test(groups = { "Functional" })
@@ -575,10 +577,14 @@ public class FeaturesFileTest
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
             fr, false);
     String gffHeader = "##gff-version 2\n";
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             true);
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
 
     /*
      * add some features
@@ -615,7 +621,9 @@ public class FeaturesFileTest
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
 
     /*
      * include non-positional features
@@ -626,7 +634,9 @@ public class FeaturesFileTest
             true);
     String expected = gffHeader
             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected),
+            exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
@@ -638,7 +648,9 @@ public class FeaturesFileTest
             false);
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * set s3dm group visible
@@ -649,7 +661,9 @@ public class FeaturesFileTest
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * now set Pfam visible
@@ -662,7 +676,14 @@ public class FeaturesFileTest
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
+  }
+
+  private String fixLineEnd(String s)
+  {
+    return s.replace("\n", System.getProperty("line.separator"));
   }
 
   /**
@@ -737,7 +758,7 @@ public class FeaturesFileTest
     visible.put("foobar", new FeatureColour(Color.blue));
     ff.outputFeatureFilters(sb, visible, featureFilters);
     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
-    assertEquals(expected, sb.toString());
+    assertEquals(fixLineEnd(expected), sb.toString());
   }
 
   /**
@@ -774,7 +795,8 @@ public class FeaturesFileTest
     String expected = gffHeader
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected), exported);
 
     /*
      * now threshold to Score > 1.1 - should exclude sf2
@@ -787,7 +809,7 @@ public class FeaturesFileTest
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * remove threshold and check sf2 is exported
@@ -797,7 +819,7 @@ public class FeaturesFileTest
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
@@ -809,7 +831,7 @@ public class FeaturesFileTest
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 
   /**
@@ -849,7 +871,9 @@ public class FeaturesFileTest
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected),
+            exported);
   
     /*
      * now threshold to Score > 1.1 - should exclude sf2
@@ -866,7 +890,9 @@ public class FeaturesFileTest
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
             + "ENDGROUP\tgrp1\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
   
     /*
      * remove threshold and check sf2 is exported
@@ -880,7 +906,7 @@ public class FeaturesFileTest
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   
     /*
      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
@@ -897,6 +923,6 @@ public class FeaturesFileTest
             + "STARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 }