align: pass the class AlignerUtils from Java to C (prototype) #8

opencb · Jun 1, 2015 · 9e38f84 · 9e38f84
1 parent 457a40c
commit 9e38f84
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Showing 14 changed files with 333 additions and 110 deletions.
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/BamAlignCommandExecutor.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/BamAlignCommandExecutor.java
@@ -19,7 +19,7 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.opencb.hpg.bigdata.core.utils.PathUtils;
-import org.opencb.hpg.bigdata.tools.tasks.alignment.mr.AlignerParams;
+import org.opencb.hpg.bigdata.core.AlignerParams;
 import org.opencb.hpg.bigdata.tools.tasks.alignment.mr.ReadAlignmentAlignMR;
 
 import java.io.IOException;

diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/FastqAlignCommandExecutor.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/FastqAlignCommandExecutor.java
@@ -19,7 +19,7 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.opencb.hpg.bigdata.core.utils.PathUtils;
-import org.opencb.hpg.bigdata.tools.tasks.alignment.mr.AlignerParams;
+import org.opencb.hpg.bigdata.core.AlignerParams;
 import org.opencb.hpg.bigdata.tools.tasks.read.mr.ReadAlignMR;
 
 import java.io.IOException;

diff --git a/hpg-bigdata-core/native/build.sh b/hpg-bigdata-core/native/build.sh
@@ -44,4 +44,4 @@ fi
 echo
 echo "Building the dynamic library $olib"
 
-gcc -O3 -std=gnu99 jni/org_opencb_hpg_bigdata_core_NativeAligner.c ./third-party/hpg-aligner/index.c ./third-party/hpg-aligner/mapper.c -o $olib -shared -fPIC -I jni/ -I $JAVA_HOME/include -I $JAVA_HOME/include/linux -I $JAVA_HOME/include/darwin
+gcc -O3 -std=gnu99 jni/org_opencb_hpg_bigdata_core_NativeAligner.c ./third-party/hpg-aligner/index.c ./third-party/hpg-aligner/mapper.c -o $olib -shared -fPIC -I jni/ -I third-party/hpg-aligner -I $JAVA_HOME/include -I $JAVA_HOME/include/linux -I $JAVA_HOME/include/darwin
diff --git a/hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeAligner.c b/hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeAligner.c
@@ -3,12 +3,118 @@
 #include <stdio.h>
 #include <malloc.h>
 
+#include "hpg-aligner.h"
+
+//------------------------------------------------------------------------------//
+
+JNIEXPORT jlong JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_load_1params
+  (JNIEnv *env, jobject this, jobject params_obj) {
+
+    aligner_params_t *params = aligner_params_new();
+
+    // get the class of the object parameter
+	jclass cls = (*env)->GetObjectClass(env, params_obj);
+
+	if (cls) {
+
+	    jfieldID fid_int, fid_float, fid_string;
+	    jstring val_string;
+	    char *str;
+
+        // get the field ID of the "numSeeds" field of this class
+	    fid_int = (*env)->GetFieldID(env, cls, "numSeeds", "I");
+	    if (fid_int) {
+    	    params->num_seeds = (*env)->GetIntField(env, params_obj, fid_int);
+    	} else {
+    	    printf("Error getting num_seeds parameter\n");
+    	}
+
+        // get the field ID of the "minSWScore" field of this class
+	    fid_float = (*env)->GetFieldID(env, cls, "minSWScore", "F");
+	    if (fid_float) {
+    	    params->min_sw_score = (*env)->GetFloatField(env, params_obj, fid_float);
+    	} else {
+    	    printf("Error getting minSWScore parameter\n");
+    	}
+
+        // get the field ID of the "seqFileName1" field of this class
+	    fid_string = (*env)->GetFieldID(env, cls, "seqFileName1", "Ljava/lang/String;");
+	    if (fid_string) {
+	        val_string = (jstring) (*env)->GetObjectField(env, params_obj, fid_string);
+	        if (val_string) {
+                str = (*env)->GetStringUTFChars(env, val_string, NULL);
+                params->seq_filename1 = strdup(str);
+                (*env)->ReleaseStringUTFChars(env, val_string, str);
+	        } else {
+                printf("Error getting String object (seqFileName1)\n");
+	        }
+    	} else {
+    	    printf("Error getting seqFileName1 parameter\n");
+    	}
+
+        // get the field ID of the "seqFileName1" field of this class
+	    fid_string = (*env)->GetFieldID(env, cls, "seqFileName1", "Ljava/lang/String;");
+	    if (fid_string) {
+	        val_string = (jstring) (*env)->GetObjectField(env, params_obj, fid_string);
+	        if (val_string) {
+                str = (*env)->GetStringUTFChars(env, val_string, NULL);
+                params->seq_filename1 = strdup(str);
+                (*env)->ReleaseStringUTFChars(env, val_string, str);
+	        } else {
+                printf("Error getting String object (seqFileName1)\n");
+	        }
+    	} else {
+    	    printf("Error getting seqFileName1 parameter\n");
+    	}
+
+        // get the field ID of the "resultFileName" field of this class
+	    fid_string = (*env)->GetFieldID(env, cls, "resultFileName", "Ljava/lang/String;");
+	    if (fid_string) {
+	        val_string = (jstring) (*env)->GetObjectField(env, params_obj, fid_string);
+	        if (val_string) {
+                str = (*env)->GetStringUTFChars(env, val_string, NULL);
+                params->out_dirname = strdup(str);
+                (*env)->ReleaseStringUTFChars(env, val_string, str);
+	        } else {
+                printf("Error getting String object (resultFileName)\n");
+	        }
+    	} else {
+    	    printf("Error getting resultFileName parameter\n");
+    	}
+
+        // get the field ID of the "indexFolderName" field of this class
+	    fid_string = (*env)->GetFieldID(env, cls, "indexFolderName", "Ljava/lang/String;");
+	    if (fid_string) {
+	        val_string = (jstring) (*env)->GetObjectField(env, params_obj, fid_string);
+	        if (val_string) {
+                str = (*env)->GetStringUTFChars(env, val_string, NULL);
+                params->index_dirname = strdup(str);
+                (*env)->ReleaseStringUTFChars(env, val_string, str);
+	        } else {
+                printf("Error getting String object (indexFolderName)\n");
+	        }
+    	} else {
+    	    printf("Error getting indexFolderName parameter\n");
+    	}
+
+    } else {
+        printf("Error getting Java class\n");
+    }
+
+    printf("Java_org_opencb_hpg_bigdata_core_NativeAligner_load_1params, params:\n");
+    aligner_params_display((aligner_params_t *) params);
+
+    return ((long) params);
+}
+
 //------------------------------------------------------------------------------//
 
-void *load_index(const char *index_path);
-void free_index(void *index);
+JNIEXPORT void JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_free_1params
+  (JNIEnv *env, jobject this, jlong params) {
+
+  aligner_params_free((aligner_params_t *) params);
+}
 
-char *map(const char *fastq, void *index);
 
 //------------------------------------------------------------------------------//
 
@@ -31,11 +137,14 @@ JNIEXPORT void JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_free_1inde
 //------------------------------------------------------------------------------//
 
 JNIEXPORT jstring JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_map
-  (JNIEnv *env, jobject this, jstring fastq, jlong index) {
+  (JNIEnv *env, jobject this, jstring fastq, jlong index, jlong params) {
 
     const char *reads = (*env)->GetStringUTFChars(env, fastq, NULL);
     char *sam = map(reads, (void *)index);
 
+    printf("Java_org_opencb_hpg_bigdata_core_NativeAligner_map, params:\n");
+    aligner_params_display((aligner_params_t *) params);
+
     jstring res = (*env)->NewStringUTF(env, sam);
 
     // free memory

diff --git a/hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeAligner.h b/hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeAligner.h
diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/hpg-aligner.c b/hpg-bigdata-core/native/third-party/hpg-aligner/hpg-aligner.c
@@ -1,12 +1,4 @@
-
-//----------------------------------------------------------------------------------------------------------------------
-//
-//----------------------------------------------------------------------------------------------------------------------
-
-void *load_index(char *index_path);
-void free_index(void *index);
-
-char *map(char *fastq, void *index);
+#include "hpg-aligner.h"
 
 //----------------------------------------------------------------------------------------------------------------------
 // main
@@ -27,4 +19,7 @@ void main() {
     // free memory
     free(sam);
     free_index(index);
-}
+}
+
+//--------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------
diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/hpg-aligner.h b/hpg-bigdata-core/native/third-party/hpg-aligner/hpg-aligner.h
@@ -0,0 +1,58 @@
+//--------------------------------------------------------------------------------
+//
+//--------------------------------------------------------------------------------
+
+typedef struct aligner_params {
+    int num_seeds;
+    float min_sw_score;
+
+    char *seq_filename1;
+    char *seq_filename2;
+    char *out_dirname;
+    char *index_dirname;
+
+} aligner_params_t;
+
+inline void aligner_params_display(aligner_params_t *params) {
+    if (params) {
+        printf("num. seeds: %i\n", params->num_seeds);
+        printf("min. SW score: %0.2f\n", params->min_sw_score);
+
+        printf("\n");
+        printf("seq. filename #1: %s\n", params->seq_filename1);
+        printf("seq. filename #2: %s\n", params->seq_filename2);
+        printf("\n");
+        printf("out dir. name  : %s\n", params->out_dirname);
+        printf("index dir. name: %s\n", params->index_dirname);
+
+    }
+}
+
+inline aligner_params_t *aligner_params_new() {
+    aligner_params_t *res = (aligner_params_t *) calloc(1, sizeof(aligner_params_t));
+    return res;
+}
+
+inline void aligner_params_free(aligner_params_t *params) {
+    if (params) {
+        printf("freeing aligner params:\n");
+        aligner_params_display(params);
+
+        if (params->seq_filename1) free(params->seq_filename1);
+        if (params->seq_filename2) free(params->seq_filename2);
+        if (params->out_dirname) free(params->out_dirname);
+        if (params->index_dirname) free(params->index_dirname);
+
+        free(params);
+    }
+}
+
+//--------------------------------------------------------------------------------
+
+void *load_index(const char *index_path);
+void free_index(void *index);
+
+char *map(const char *fastq, void *index);
+
+//--------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------
diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/index.c b/hpg-bigdata-core/native/third-party/hpg-aligner/index.c
@@ -23,3 +23,6 @@ void free_index(void *index) {
         free((char *) index);
     }
 }
+
+//--------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------
diff --git a/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c b/hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c
@@ -17,3 +17,6 @@ char *map(const char *fastq, char *index_path) {
     //printf("Mapping...\n%s\n%s\n...done!\n", fastq, sam);
     return sam;
 }
+
+//--------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------
diff --git a/...ols/tasks/alignment/mr/AlignerParams.java → ...pencb/hpg/bigdata/core/AlignerParams.java b/...ols/tasks/alignment/mr/AlignerParams.java → ...pencb/hpg/bigdata/core/AlignerParams.java
@@ -1,11 +1,12 @@
-package org.opencb.hpg.bigdata.tools.tasks.alignment.mr;
+package org.opencb.hpg.bigdata.core;
 
 /**
  * Created by jtarraga on 29/05/15.
  */
 public class AlignerParams {
     public int numSeeds;
     public float minSWScore;
+
     public String seqFileName1;
     public String seqFileName2;
     public String resultFileName;
@@ -14,9 +15,10 @@ public class AlignerParams {
     public AlignerParams() {
         numSeeds = 20;
         minSWScore = 0.8f;
-        seqFileName1 = null;
-        seqFileName2 = null;
-        resultFileName = null;
-        indexFolderName = null;
+
+        seqFileName1 = new String("no-file-specified!");
+        seqFileName2 = new String("no-file-specified!");
+        resultFileName = new String("no-file-specified!");
+        indexFolderName = new String("no-file-specified!");
     }
 }
diff --git a/hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/NativeAligner.java b/hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/NativeAligner.java
@@ -17,10 +17,14 @@
 package org.opencb.hpg.bigdata.core;
 
 public class NativeAligner {
+	// params
+	public native long load_params(AlignerParams paramsObj);
+	public native void free_params(long params);
+
 	// index
 	public native long load_index(String indexPath);
 	public native void free_index(long index);
 
 	// map
-	public native String map(String sequences, long index);
+	public native String map(String sequences, long index, long params);
 }