Sort TIFF files by well label

...instead of strictly alphabetically.  This allows the wells to appear
in "A1, A2, ..., A10" order, instead of "A1, A10, A2, ..." order.

Noticed by Rubén Muñoz.  Closes #7950.

To test:

ant -Dtestng.directory=$DATA/scanr/ test-automated

components/bio-formats/src/loci/formats/in/ScanrReader.java

@@ -23,9 +23,11 @@
 
 package loci.formats.in;
 
+import java.io.File;
 import java.io.IOException;
 import java.nio.ByteOrder;
 import java.util.Arrays;
+import java.util.Comparator;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -362,7 +364,42 @@ else if (!isGroupFiles() && checkSuffix(id, "tif")) {
     }
 
     tiffs = new String[nChannels * nWells * nPos * nTimepoints * nSlices];
-    Arrays.sort(list);
+
+    Arrays.sort(list, new Comparator<String>() {
+      public int compare(String s1, String s2) {
+        int lastSeparator1 = s1.lastIndexOf(File.separator) + 1;
+        int lastSeparator2 = s2.lastIndexOf(File.separator) + 1;
+        String dir1 = s1.substring(0, lastSeparator1);
+        String dir2 = s2.substring(0, lastSeparator2);
+
+        if (!dir1.equals(dir2)) {
+          return dir1.compareTo(dir2);
+        }
+
+        int dash1 = s1.indexOf("-", lastSeparator1);
+        int dash2 = s2.indexOf("-", lastSeparator2);
+
+        String label1 = dash1 < 0 ? "" : s1.substring(lastSeparator1, dash1);
+        String label2 = dash2 < 0 ? "" : s2.substring(lastSeparator2, dash2);
+
+        if (label1.equals(label2)) {
+          String remainder1 = dash1 < 0 ? s1 : s1.substring(dash1);
+          String remainder2 = dash2 < 0 ? s2 : s2.substring(dash2);
+          return remainder1.compareTo(remainder2);
+        }
+
+        Integer index1 = wellLabels.get(label1);
+        Integer index2 = wellLabels.get(label2);
+
+        if (index1 == null && index2 != null) {
+          return 1;
+        }
+        else if (index1 != null && index2 == null) {
+          return -1;
+        }
+        return index1.compareTo(index2);
+      }
+    });
     int lastListIndex = 0;
 
     int next = 0;