JAL-2629 can now choose number of jackhmmer iterations

[jalview.git] / src / jalview / util / FileUtils.java

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 3652448..7e607ab 100644 (file)
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -2,11 +2,14 @@ package jalview.util;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.DirectoryStream;
 import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
+import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -85,24 +88,26 @@ public final class FileUtils
    * Answers a (possibly empty) list of file paths found by searching below
    * <code>from</code> that match the supplied regular expression
    * <code>pattern</code>. Results may include <code>from</code> itself if it
-   * matches. If an exception occurs it is written to syserr and any results up
-   * to that point are returned. Note that the regular expression match applies
-   * to the whole path of any matched file.
+   * matches. If an exception occurs it is written to syserr and any results up to
+   * that point are returned. Note that the regular expression match applies to
+   * the whole path of any matched file.
    * <p>
-   * Because the whole directory tree below <code>from</code> is searched, this
-   * method may be slow if used for a high level directory.
+   * WARNING: because the whole directory tree below <code>from</code> is
+   * searched, this method may be slow if used for a high level directory, or may
+   * exit prematurely if security or other exceptions occur.
    * 
    * <pre>
    * Example: 
-   *   findMatchingPaths(".*&#47chimera.exe$", Paths.get("C:/Program Files"))
+   *   findMatchingPaths(Paths.get("C:/Program Files"), ".*&#47chimera.exe$")
    * </pre>
    * 
-   * @param pattern
    * @param from
+   * @param pattern
+   * 
    * @return
    * @see https://stackoverflow.com/questions/794381/how-to-find-files-that-match-a-wildcard-string-in-java/31685610#comment62441832_31685610
    */
-  public static List<String> findMatchingPaths(String pattern, Path from)
+  public static List<String> findMatchingPaths(Path from, String pattern)
   {
     List<String> matches = new ArrayList<>();
     PathMatcher pathMatcher = FileSystems.getDefault()
@@ -119,4 +124,85 @@ public final class FileUtils
 
     return matches;
   }
+
+  /**
+   * Answers a (possibly empty) list of paths to files below the given root path,
+   * that match the given pattern. The pattern should be a '/' delimited set of
+   * glob patterns, each of which is used to match child file names (not full
+   * paths). Note that 'directory spanning' glob patterns (**) are <em>not</em>
+   * supported by this method.
+   * <p>
+   * For example
+   * 
+   * <pre>
+   *   findMatches("C:\\", "Program Files*&#47Chimera*&#47bin/{chimera,chimera.exe}"
+   * </pre>
+   * 
+   * would match "C:\Program Files\Chimera 1.11\bin\chimera.exe" and "C:\Program
+   * Files (x86)\Chimera 1.10.1\bin\chimera"
+   * 
+   * @param root
+   * @param pattern
+   * @return
+   * @see https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+   */
+  public static List<String> findMatches(String root, String pattern)
+  {
+    List<String> results = new ArrayList<>();
+    try
+    {
+      Path from = Paths.get(root);
+      findMatches(results, from, Arrays.asList(pattern.split("/")));
+    } catch (Throwable e)
+    {
+      // Paths.get can throw IllegalArgumentException
+      System.err.println(String.format("Error searching %s for %s: %s",
+              root, pattern, e.toString()));
+    }
+
+    return results;
+  }
+
+  /**
+   * A helper method that performs recursive search of file patterns and adds any
+   * 'leaf node' matches to the results list
+   * 
+   * @param results
+   * @param from
+   * @param patterns
+   */
+  protected static void findMatches(List<String> results, Path from,
+          List<String> patterns)
+  {
+    if (patterns.isEmpty())
+    {
+      /*
+       * reached end of recursion with all components matched
+       */
+      results.add(from.toString());
+      return;
+    }
+
+    String pattern = patterns.get(0);
+    try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(from,
+            pattern))
+    {
+      dirStream.forEach(p -> {
+
+        /*
+         * matched a next level file - search below it
+         * (ignore non-directory non-leaf matches)
+         */
+        List<String> subList = patterns.subList(1, patterns.size());
+        if (subList.isEmpty() || p.toFile().isDirectory())
+        {
+          findMatches(results, p, subList);
+        }
+      });
+    } catch (IOException e)
+    {
+      System.err.println(String.format("Error searching %s: %s", pattern,
+              e.toString()));
+    }
+  }
 }