From 25e36b8f366dab01f838d8175e59e9148628eb68 Mon Sep 17 00:00:00 2001
From: BobHanson <hansonr@stolaf.edu>
Date: Mon, 1 Jun 2020 12:23:58 -0500
Subject: [PATCH] JAL-3626 reconciled Platform

 - replaces escapeString with escapeBackslashes

 - adds pathEquals
---
 src/jalview/gui/AppJmol.java                       |    4 +-
 src/jalview/gui/ChimeraViewFrame.java              |    2 +-
 src/jalview/project/Jalview2XML.java               |    3 +-
 .../structure/StructureSelectionManager.java       |    4 +-
 src/jalview/util/Platform.java                     |   45 ++++++++++++++------
 5 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5687219..1698bf8 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -330,7 +330,7 @@ public class AppJmol extends StructureViewerBase
     for (String s : files)
     {
       fileList.append(SPACE).append(QUOTE)
-              .append(Platform.escapeString(s)).append(QUOTE);
+              .append(Platform.escapeBackslashes(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -524,7 +524,7 @@ public class AppJmol extends StructureViewerBase
             addingStructures = true; // already files loaded.
             for (int c = 0; c < filesInViewer.length; c++)
             {
-              if (filesInViewer[c].equals(file))
+              if (Platform.pathEquals(filesInViewer[c], file))
               {
                 file = null;
                 break;
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index fff1eed..317eff5 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -481,7 +481,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         {
           filePDB.add(thePdbEntry);
           filePDBpos.add(Integer.valueOf(pi));
-          files.append(" \"" + Platform.escapeString(file) + "\"");
+          files.append(" \"" + Platform.escapeBackslashes(file) + "\"");
         }
       }
     } catch (OutOfMemoryError oomerror)
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index b0315e8..c28002f 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4694,7 +4694,8 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+        newFileLoc
+                .append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 82d66f2..66bd085 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -43,6 +43,7 @@ import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
@@ -1202,7 +1203,8 @@ public class StructureSelectionManager implements ApplicationSingletonI
     StringBuilder sb = new StringBuilder(64);
     for (StructureMapping sm : mappings)
     {
-      if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+      if (Platform.pathEquals(sm.pdbfile, pdbfile)
+              && seqs.contains(sm.sequence))
       {
         sb.append(sm.mappingDetails);
         sb.append(NEWLINE);
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index c511ce3..728110e 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -158,23 +158,17 @@ public class Platform
   }
 
   /**
-   * escape a string according to the local platform's escape character
+   * An earlier version of escapeString()? Looks fine to me -- BH
    * 
-   * @param file
-   * @return escaped file
+   * Answers the input with every backslash replaced with a double backslash (an
+   * 'escaped' single backslash)
+   * 
+   * @param s
+   * @return
    */
-  public static String escapeString(String file)
+  public static String escapeBackslashes(String s)
   {
-    StringBuffer f = new StringBuffer();
-    int p = 0, lastp = 0;
-    while ((p = file.indexOf('\\', lastp)) > -1)
-    {
-      f.append(file.subSequence(lastp, p));
-      f.append("\\\\");
-      lastp = p + 1;
-    }
-    f.append(file.substring(lastp));
-    return f.toString();
+    return s == null ? null : s.replace("\\", "\\\\");
   }
 
   /**
@@ -714,6 +708,29 @@ public class Platform
 
   }
 
+  /**
+   * A (case sensitive) file path comparator that ignores the difference between
+   * / and \
+   * 
+   * @param path1
+   * @param path2
+   * @return
+   */
+  public static boolean pathEquals(String path1, String path2)
+  {
+    if (path1 == null)
+    {
+      return path2 == null;
+    }
+    if (path2 == null)
+    {
+      return false;
+    }
+    String p1 = path1.replace('\\', '/');
+    String p2 = path2.replace('\\', '/');
+    return p1.equals(p2);
+  }
+
   public static URL getDocumentBase()
   {
     return (isJS ? jsutil.getDocumentBase() : null);
-- 
1.7.10.2