From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Mon, 4 Feb 2019 14:48:05 +0000 (-0600)
Subject: fixing array processing order
X-Git-Tag: Release_2_11_4_0~45^2~18^2~256
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3ca62ac09227ae36e2197050e8910382ea30f3fe;p=jalview.git

fixing array processing order

- does point out an issue with hiddenColumns joining adjacent hides
sometimes but not other times.
---

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 427ad8f..e0f28bb 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -601,7 +601,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
     {
       String[] seqRefs = hiddenSeqs.split(";");
-      for (int i = seqRefs.length; --i >= 0;)
+      for (int i = 0, n = seqRefs.length; i < n; i++)
       {
         hiddenSeqRefs.add(seqRefs[i]);
       }
@@ -615,7 +615,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
-      for (int i = rangeStrings.length; --i >= 0;)
+      for (int i = 0, n = rangeStrings.length; i < n; i++)
       {
         String[] range = rangeStrings[i].split("-");
         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 560a6a8..2d5f7a2 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -236,7 +236,7 @@ public class JSONFileTest
       testAlignment = formatAdapter.readFile(jsonOutput,
               DataSourceType.PASTE, FileFormat.Json);
       testJsonFile = (JSONFile) formatAdapter.getAlignFile();
-      // System.out.println(jsonOutput);
+      System.out.println(jsonOutput);
     } catch (IOException e)
     {
       e.printStackTrace();