Compatible deserialisation of previous version vdjca files.

milaboratory · Oct 1, 2015 · 7d877d8 · 7d877d8
1 parent 2934621
commit 7d877d8
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Showing 3 changed files with 67 additions and 3 deletions.
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java
@@ -32,13 +32,13 @@
 import com.milaboratory.core.io.CompressionType;
 import com.milaboratory.mixcr.reference.Allele;
 import com.milaboratory.mixcr.reference.AlleleResolver;
+import com.milaboratory.mixcr.reference.CompatibilityIO;
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.util.CanReportProgress;
 import com.milaboratory.util.CountingInputStream;
 
 import java.io.*;
-import java.util.Arrays;
 import java.util.List;
 
 import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.*;
@@ -86,8 +86,16 @@ public void init() {
         assert MAGIC_BYTES.length == MAGIC_LENGTH;
         byte[] magic = new byte[MAGIC_LENGTH];
         input.readFully(magic);
-        if (!Arrays.equals(magic, MAGIC_BYTES))
-            throw new RuntimeException("Unsupported file format; .vdjca file of version " + new String(magic) + " while you are running MiXCR " + MAGIC);
+        String magicString = new String(magic);
+        switch (magicString) {
+            case MAGIC_V3:
+                CompatibilityIO.registerV3Serializers(input.getSerializersManager());
+                break;
+            case MAGIC:
+                break;
+            default:
+                throw new RuntimeException("Unsupported file format; .vdjca file of version " + new String(magic) + " while you are running MiXCR " + MAGIC);
+        }
 
         parameters = input.readObject(VDJCAlignerParameters.class);
 

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java
@@ -40,6 +40,7 @@
 import java.util.List;
 
 public final class VDJCAlignmentsWriter implements AutoCloseable {
+    static final String MAGIC_V3 = "MiXCR.VDJC.V03";
     static final String MAGIC = "MiXCR.VDJC.V04";
     static final int MAGIC_LENGTH = 14;
     static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII);

diff --git a/src/main/java/com/milaboratory/mixcr/reference/CompatibilityIO.java b/src/main/java/com/milaboratory/mixcr/reference/CompatibilityIO.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
+ * (here and after addressed as Inventors)
+ * All Rights Reserved
+ *
+ * Permission to use, copy, modify and distribute any part of this program for
+ * educational, research and non-profit purposes, by non-profit institutions
+ * only, without fee, and without a written agreement is hereby granted,
+ * provided that the above copyright notice, this paragraph and the following
+ * three paragraphs appear in all copies.
+ *
+ * Those desiring to incorporate this work into commercial products or use for
+ * commercial purposes should contact the Inventors using one of the following
+ * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com
+ *
+ * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
+ * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
+ * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS
+ * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
+ * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO
+ * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
+ * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
+ * PATENT, TRADEMARK OR OTHER RIGHTS.
+ */
+package com.milaboratory.mixcr.reference;
+
+import com.milaboratory.primitivio.DefaultSerializersProviderImpl;
+import com.milaboratory.primitivio.SerializersManager;
+
+import static com.milaboratory.mixcr.reference.BasicReferencePoint.*;
+import static com.milaboratory.mixcr.reference.BasicReferencePoint.CEnd;
+
+/**
+ * Created by dbolotin on 30/09/15.
+ */
+public final class CompatibilityIO {
+    private CompatibilityIO() {
+    }
+
+    public static void registerV3Serializers(SerializersManager manager) {
+        manager.registerCustomSerializer(BasicReferencePoint.class,
+                new DefaultSerializersProviderImpl.CustomEnumSerializer<>(
+                        BasicReferencePoint.class,
+                        V5UTRBegin, V5UTREndL1Begin, L1EndVIntronBegin, VIntronEndL2Begin,
+                        L2EndFR1Begin, FR1EndCDR1Begin, CDR1EndFR2Begin, FR2EndCDR2Begin,
+                        CDR2EndFR3Begin, FR3EndCDR3Begin, VEndTrimmed, VEnd, DBegin,
+                        DBeginTrimmed, DEndTrimmed, DEnd, JBegin, JBeginTrimmed,
+                        CDR3EndFR4Begin, FR4End, CBegin, CExon1End, CEnd
+                ));
+    }
+}