From 187dc0d09071687d3975c052b6e63067c5804937 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20=C5=BBok?= <Tomasz.Zok@cs.put.poznan.pl>
Date: Thu, 25 Oct 2018 14:49:54 +0200
Subject: [PATCH 1/3] update versions for hotfix

---
 mcq-cli/pom.xml        | 2 +-
 mcq-clustering/pom.xml | 2 +-
 mcq-core/pom.xml       | 2 +-
 mcq-gui/pom.xml        | 2 +-
 pom.xml                | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/mcq-cli/pom.xml b/mcq-cli/pom.xml
index e4b08e97..f7fbfef5 100644
--- a/mcq-cli/pom.xml
+++ b/mcq-cli/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>mcq-parent</artifactId>
     <groupId>pl.poznan.put</groupId>
-    <version>1.4</version>
+    <version>1.4.1</version>
   </parent>
 
   <artifactId>mcq-cli</artifactId>
diff --git a/mcq-clustering/pom.xml b/mcq-clustering/pom.xml
index f6e5b0c2..198c416d 100644
--- a/mcq-clustering/pom.xml
+++ b/mcq-clustering/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>mcq-parent</artifactId>
     <groupId>pl.poznan.put</groupId>
-    <version>1.4</version>
+    <version>1.4.1</version>
   </parent>
 
   <artifactId>mcq-clustering</artifactId>
diff --git a/mcq-core/pom.xml b/mcq-core/pom.xml
index 244634a1..8905a0bb 100644
--- a/mcq-core/pom.xml
+++ b/mcq-core/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>mcq-parent</artifactId>
     <groupId>pl.poznan.put</groupId>
-    <version>1.4</version>
+    <version>1.4.1</version>
   </parent>
 
   <artifactId>mcq-core</artifactId>
diff --git a/mcq-gui/pom.xml b/mcq-gui/pom.xml
index 78e5c461..3274fd28 100644
--- a/mcq-gui/pom.xml
+++ b/mcq-gui/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>mcq-parent</artifactId>
     <groupId>pl.poznan.put</groupId>
-    <version>1.4</version>
+    <version>1.4.1</version>
   </parent>
 
   <artifactId>mcq-gui</artifactId>
diff --git a/pom.xml b/pom.xml
index c089e242..ded7be62 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>pl.poznan.put</groupId>
   <artifactId>mcq-parent</artifactId>
-  <version>1.4</version>
+  <version>1.4.1</version>
   <packaging>pom</packaging>
 
   <modules>

From 163327f27f5721a44a061bb8671ba40ea90b8916 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20=C5=BBok?= <Tomasz.Zok@cs.put.poznan.pl>
Date: Thu, 25 Oct 2018 14:50:33 +0200
Subject: [PATCH 2/3] Update scripts

---
 mcq-cli/global | 2 +-
 mcq-cli/lcs    | 2 +-
 mcq-cli/local  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/mcq-cli/global b/mcq-cli/global
index db89f406..bb175948 100755
--- a/mcq-cli/global
+++ b/mcq-cli/global
@@ -1,2 +1,2 @@
 #! /bin/bash
-exec java -cp $(dirname $0)/target/mcq-cli-1.4-SNAPSHOT-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Global $@
+exec java -cp $(dirname $0)/target/mcq-cli-1.4.1-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Global $@
diff --git a/mcq-cli/lcs b/mcq-cli/lcs
index 3415ac2c..b6bfac38 100755
--- a/mcq-cli/lcs
+++ b/mcq-cli/lcs
@@ -1,2 +1,2 @@
 #! /bin/bash
-exec java -cp $(dirname $0)/target/mcq-cli-1.4-SNAPSHOT-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Lcs $@
+exec java -cp $(dirname $0)/target/mcq-cli-1.4.1-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Lcs $@
diff --git a/mcq-cli/local b/mcq-cli/local
index 866d5524..240a24cb 100755
--- a/mcq-cli/local
+++ b/mcq-cli/local
@@ -1,2 +1,2 @@
 #! /bin/bash
-exec java -cp $(dirname $0)/target/mcq-cli-1.4-SNAPSHOT-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Local $@
+exec java -cp $(dirname $0)/target/mcq-cli-1.4.1-jar-with-dependencies.jar pl.poznan.put.mcq.cli.Local $@

From ddb65903e891064f58d55d2449d7039fdc804c82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20=C5=BBok?= <Tomasz.Zok@cs.put.poznan.pl>
Date: Thu, 25 Oct 2018 15:00:34 +0200
Subject: [PATCH 3/3] Cluster and visualize only for more than 2 structures

---
 .../java/pl/poznan/put/mcq/cli/Global.java    | 29 +++++++++++--------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java b/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java
index c21a9aea..6e7613c5 100644
--- a/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java
+++ b/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java
@@ -68,7 +68,7 @@ private Global() {
   private static final class Listener implements ParallelGlobalComparator.ProgressListener {
     private final ProgressBar progressBar;
 
-    public Listener(final ProgressBar progressBar) {
+    private Listener(final ProgressBar progressBar) {
       super();
       this.progressBar = progressBar;
     }
@@ -80,20 +80,25 @@ public void setProgress(final int progress) {
 
     @Override
     public void complete(final GlobalMatrix matrix) {
-      progressBar.close();
-
-      final PrototypeBasedClusterer clusterer = new KMedoids();
-      final double[][] rawMatrix = matrix.getDistanceMatrix().getMatrix();
-      final ScoredClusteringResult clustering =
-          KScanner.parallelScan(clusterer, rawMatrix, PAM.getInstance());
-      final PartitionalClustering partitionalClustering =
-          new PartitionalClustering(matrix.getDistanceMatrix(), clustering);
-
       try {
+        progressBar.close();
+
         final File directory = ExecHelper.createRandomDirectory();
         Listener.exportResults(directory, matrix);
-        Listener.exportDrawing(directory, partitionalClustering);
-        Listener.exportClustering(directory, partitionalClustering);
+
+        final double[][] rawMatrix = matrix.getDistanceMatrix().getMatrix();
+
+        if (rawMatrix.length > 2) {
+          final PrototypeBasedClusterer clusterer = new KMedoids();
+          final ScoredClusteringResult clustering =
+              KScanner.parallelScan(clusterer, rawMatrix, PAM.getInstance());
+          final PartitionalClustering partitionalClustering =
+              new PartitionalClustering(matrix.getDistanceMatrix(), clustering);
+
+          Listener.exportDrawing(directory, partitionalClustering);
+          Listener.exportClustering(directory, partitionalClustering);
+        }
+
         System.out.println("Results available in: " + directory);
       } catch (final IOException e) {
         System.err.println("Failed to store results");