Update btllib in RResolver

Author: schutzekatze

RResolver/btllib/extras/java/SWIGTYPE_p_btllib__CString.java

@@ -0,0 +1,26 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 4.0.2
+ *
+ * Do not make changes to this file unless you know what you are doing--modify
+ * the SWIG interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+package btllib;
+
+public class SWIGTYPE_p_btllib__CString {
+  private transient long swigCPtr;
+
+  protected SWIGTYPE_p_btllib__CString(long cPtr, @SuppressWarnings("unused") boolean futureUse) {
+    swigCPtr = cPtr;
+  }
+
+  protected SWIGTYPE_p_btllib__CString() {
+    swigCPtr = 0;
+  }
+
+  protected static long getCPtr(SWIGTYPE_p_btllib__CString obj) {
+    return (obj == null) ? 0 : obj.swigCPtr;
+  }
+}
+

RResolver/btllib/extras/java/SeqReader.java

@@ -229,7 +229,6 @@ public SeqReader.RecordIterator end() {
   public final static class Format {
     public final static SeqReader.Format UNDETERMINED = new SeqReader.Format("UNDETERMINED");
     public final static SeqReader.Format FASTA = new SeqReader.Format("FASTA");
-    public final static SeqReader.Format MULTILINE_FASTA = new SeqReader.Format("MULTILINE_FASTA");
     public final static SeqReader.Format FASTQ = new SeqReader.Format("FASTQ");
     public final static SeqReader.Format SAM = new SeqReader.Format("SAM");
     public final static SeqReader.Format GFA2 = new SeqReader.Format("GFA2");
@@ -269,7 +268,7 @@ private Format(String swigName, Format swigEnum) {
       swigNext = this.swigValue+1;
     }
 
-    private static Format[] swigValues = { UNDETERMINED, FASTA, MULTILINE_FASTA, FASTQ, SAM, GFA2, INVALID };
+    private static Format[] swigValues = { UNDETERMINED, FASTA, FASTQ, SAM, GFA2, INVALID };
     private static int swigNext = 0;
     private final int swigValue;
     private final String swigName;

RResolver/btllib/extras/java/SeqReaderMultilineFastqModule.java

@@ -0,0 +1,43 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 4.0.2
+ *
+ * Do not make changes to this file unless you know what you are doing--modify
+ * the SWIG interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+package btllib;
+
+public class SeqReaderMultilineFastqModule {
+  private transient long swigCPtr;
+  protected transient boolean swigCMemOwn;
+
+  protected SeqReaderMultilineFastqModule(long cPtr, boolean cMemoryOwn) {
+    swigCMemOwn = cMemoryOwn;
+    swigCPtr = cPtr;
+  }
+
+  protected static long getCPtr(SeqReaderMultilineFastqModule obj) {
+    return (obj == null) ? 0 : obj.swigCPtr;
+  }
+
+  @SuppressWarnings("deprecation")
+  protected void finalize() {
+    delete();
+  }
+
+  public synchronized void delete() {
+    if (swigCPtr != 0) {
+      if (swigCMemOwn) {
+        swigCMemOwn = false;
+        btllibJNI.delete_SeqReaderMultilineFastqModule(swigCPtr);
+      }
+      swigCPtr = 0;
+    }
+  }
+
+  public SeqReaderMultilineFastqModule() {
+    this(btllibJNI.new_SeqReaderMultilineFastqModule(), true);
+  }
+
+}

RResolver/btllib/extras/java/btllib.java

@@ -568,15 +568,27 @@ public static String join(SWIGTYPE_p_std__vectorT_std__string_t s, String delim)
   }
 
   public static void ltrim(SWIGTYPE_p_std__string s) {
-    btllibJNI.ltrim(SWIGTYPE_p_std__string.getCPtr(s));
+    btllibJNI.ltrim__SWIG_0(SWIGTYPE_p_std__string.getCPtr(s));
+  }
+
+  public static void ltrim(SWIGTYPE_p_btllib__CString s) {
+    btllibJNI.ltrim__SWIG_1(SWIGTYPE_p_btllib__CString.getCPtr(s));
   }
 
   public static void rtrim(SWIGTYPE_p_std__string s) {
-    btllibJNI.rtrim(SWIGTYPE_p_std__string.getCPtr(s));
+    btllibJNI.rtrim__SWIG_0(SWIGTYPE_p_std__string.getCPtr(s));
+  }
+
+  public static void rtrim(SWIGTYPE_p_btllib__CString s) {
+    btllibJNI.rtrim__SWIG_1(SWIGTYPE_p_btllib__CString.getCPtr(s));
   }
 
   public static void trim(SWIGTYPE_p_std__string s) {
-    btllibJNI.trim(SWIGTYPE_p_std__string.getCPtr(s));
+    btllibJNI.trim__SWIG_0(SWIGTYPE_p_std__string.getCPtr(s));
+  }
+
+  public static void trim(SWIGTYPE_p_btllib__CString s) {
+    btllibJNI.trim__SWIG_1(SWIGTYPE_p_btllib__CString.getCPtr(s));
   }
 
   public static boolean startswith(String s, String prefix) {

RResolver/btllib/extras/java/btllibJNI.java

@@ -218,6 +218,8 @@ public class btllibJNI {
   public final static native void calc_minimizer(long jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8);
   public final static native long new_SeqReaderFastqModule();
   public final static native void delete_SeqReaderFastqModule(long jarg1);
+  public final static native long new_SeqReaderMultilineFastqModule();
+  public final static native void delete_SeqReaderMultilineFastqModule(long jarg1);
   public final static native long new_SeqReaderFastaModule();
   public final static native void delete_SeqReaderFastaModule(long jarg1);
   public final static native long new_SeqReaderMultilineFastaModule();
@@ -373,9 +375,12 @@ public class btllibJNI {
   public final static native String get_strerror();
   public final static native long split(String jarg1, String jarg2);
   public final static native String join(long jarg1, String jarg2);
-  public final static native void ltrim(long jarg1);
-  public final static native void rtrim(long jarg1);
-  public final static native void trim(long jarg1);
+  public final static native void ltrim__SWIG_0(long jarg1);
+  public final static native void ltrim__SWIG_1(long jarg1);
+  public final static native void rtrim__SWIG_0(long jarg1);
+  public final static native void rtrim__SWIG_1(long jarg1);
+  public final static native void trim__SWIG_0(long jarg1);
+  public final static native void trim__SWIG_1(long jarg1);
   public final static native boolean startswith(String jarg1, String jarg2);
   public final static native boolean endswith(String jarg1, String jarg2);
   public final static native long DataSource_SWIGUpcast(long jarg1);

RResolver/btllib/extras/java/btllib_wrap.cxx

@@ -240,6 +240,7 @@ static void SWIGUNUSED SWIG_JavaThrowException(JNIEnv *jenv, SWIG_JavaExceptionC
 #include "btllib/counting_bloom_filter.hpp"
 #include "btllib/indexlr.hpp"
 #include "btllib/seq_reader_fastq_module.hpp"
+#include "btllib/seq_reader_multiline_fastq_module.hpp"
 #include "btllib/seq_reader_fasta_module.hpp"
 #include "btllib/seq_reader_multiline_fasta_module.hpp"
 #include "btllib/nthash.hpp"
@@ -3837,6 +3838,28 @@ SWIGEXPORT void JNICALL Java_btllib_btllibJNI_delete_1SeqReaderFastqModule(JNIEn
 }
 
 
+SWIGEXPORT jlong JNICALL Java_btllib_btllibJNI_new_1SeqReaderMultilineFastqModule(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  btllib::SeqReaderMultilineFastqModule *result = 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (btllib::SeqReaderMultilineFastqModule *)new btllib::SeqReaderMultilineFastqModule();
+  *(btllib::SeqReaderMultilineFastqModule **)&jresult = result; 
+  return jresult;
+}
+
+
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_delete_1SeqReaderMultilineFastqModule(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  btllib::SeqReaderMultilineFastqModule *arg1 = (btllib::SeqReaderMultilineFastqModule *) 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(btllib::SeqReaderMultilineFastqModule **)&jarg1; 
+  delete arg1;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_btllib_btllibJNI_new_1SeqReaderFastaModule(JNIEnv *jenv, jclass jcls) {
   jlong jresult = 0 ;
   btllib::SeqReaderFastaModule *result = 0 ;
@@ -7858,7 +7881,7 @@ SWIGEXPORT jstring JNICALL Java_btllib_btllibJNI_join(JNIEnv *jenv, jclass jcls,
 }
 
 
-SWIGEXPORT void JNICALL Java_btllib_btllibJNI_ltrim(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_ltrim_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   std::string *arg1 = 0 ;
 
   (void)jenv;
@@ -7872,7 +7895,21 @@ SWIGEXPORT void JNICALL Java_btllib_btllibJNI_ltrim(JNIEnv *jenv, jclass jcls, j
 }
 
 
-SWIGEXPORT void JNICALL Java_btllib_btllibJNI_rtrim(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_ltrim_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  btllib::CString *arg1 = 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(btllib::CString **)&jarg1;
+  if (!arg1) {
+    SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "btllib::CString & reference is null");
+    return ;
+  } 
+  btllib::ltrim(*arg1);
+}
+
+
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_rtrim_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   std::string *arg1 = 0 ;
 
   (void)jenv;
@@ -7886,7 +7923,21 @@ SWIGEXPORT void JNICALL Java_btllib_btllibJNI_rtrim(JNIEnv *jenv, jclass jcls, j
 }
 
 
-SWIGEXPORT void JNICALL Java_btllib_btllibJNI_trim(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_rtrim_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  btllib::CString *arg1 = 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(btllib::CString **)&jarg1;
+  if (!arg1) {
+    SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "btllib::CString & reference is null");
+    return ;
+  } 
+  btllib::rtrim(*arg1);
+}
+
+
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_trim_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   std::string *arg1 = 0 ;
 
   (void)jenv;
@@ -7900,6 +7951,20 @@ SWIGEXPORT void JNICALL Java_btllib_btllibJNI_trim(JNIEnv *jenv, jclass jcls, jl
 }
 
 
+SWIGEXPORT void JNICALL Java_btllib_btllibJNI_trim_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  btllib::CString *arg1 = 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(btllib::CString **)&jarg1;
+  if (!arg1) {
+    SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "btllib::CString & reference is null");
+    return ;
+  } 
+  btllib::trim(*arg1);
+}
+
+
 SWIGEXPORT jboolean JNICALL Java_btllib_btllibJNI_startswith(JNIEnv *jenv, jclass jcls, jstring jarg1, jstring jarg2) {
   jboolean jresult = 0 ;
   std::string arg1 ;

RResolver/btllib/extras/java/meson.build

@@ -27,5 +27,5 @@ btllib_java = shared_module('btllib',
                              install_dir : 'java')
 
 # Next line is automatically generated by java wrapper script, do not modify
-java_files = ['./SWIGTYPE_p_unsigned_int.java','./SWIGTYPE_p_pid_t.java','./btllib.java','./SWIGTYPE_p_std__mapT_unsigned_long_btllib__ProcessPipelineInternal_t.java','./btllibJNI.java','./DataSource.java','./SWIGTYPE_p_std__string.java','./SWIGTYPE_p_std__vectorT_unsigned_char_t.java','./SWIGTYPE_p_std__ifstream.java','./SWIGTYPE_p_bool.java','./SWIGTYPE_p_std__vectorT_unsigned_int_t.java','./SWIGTYPE_p_std__vectorT_bool_t.java','./SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_int_t_t.java','./SeqReaderFastqModule.java','./SWIGTYPE_p_std__vectorT_unsigned_long_long_t.java','./SWIGTYPE_p_std__vectorT_btllib__IORedirection_t.java','./SWIGTYPE_p_FILE.java','./BloomFilter.java','./SWIGTYPE_p_unsigned_long_long.java','./SeedNtHash.java','./SeqReader.java','./KmerBloomFilter.java','./SWIGTYPE_p_p_unsigned_long_long.java','./SeqWriter.java','./SWIGTYPE_p_p_btllib__Indexlr__Minimizer.java','./SWIGTYPE_p_std__arrayT_int_2_t.java','./SWIGTYPE_p_std__vectorT_btllib__Indexlr__Minimizer_t.java','./SWIGTYPE_p_std__vectorT_SpacedSeed_t.java','./SeqReaderSamModule.java','./SWIGTYPE_p_btllib__IORedirection.java','./SeqReaderFastaModule.java','./SWIGTYPE_p_int.java','./SWIGTYPE_p_p_FILE.java','./ProcessPipelineInternal.java','./NtHash.java','./SWIGTYPE_p_std__shared_ptrT_cpptoml__table_t.java','./SWIGTYPE_p_mode_t.java','./SeqReaderMultilineFastaModule.java','./Datatype.java','./SWIGTYPE_p_ssize_t.java','./SWIGTYPE_p_std__mutex.java','./SWIGTYPE_p_unsigned_char.java','./Indexlr.java','./SeqReaderGfa2Module.java','./SWIGTYPE_p_std__vectorT_std__string_t.java','./SWIGTYPE_p_std__ios.java','./DataStream.java','./SeedBloomFilter.java','./DataSink.java']
+java_files = ['./SWIGTYPE_p_unsigned_int.java','./SWIGTYPE_p_pid_t.java','./btllib.java','./SWIGTYPE_p_std__mapT_unsigned_long_btllib__ProcessPipelineInternal_t.java','./btllibJNI.java','./DataSource.java','./SWIGTYPE_p_std__string.java','./SWIGTYPE_p_std__vectorT_unsigned_char_t.java','./SWIGTYPE_p_std__ifstream.java','./SWIGTYPE_p_bool.java','./SWIGTYPE_p_std__vectorT_unsigned_int_t.java','./SWIGTYPE_p_std__vectorT_bool_t.java','./SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_int_t_t.java','./SeqReaderFastqModule.java','./SWIGTYPE_p_std__vectorT_unsigned_long_long_t.java','./SWIGTYPE_p_std__vectorT_btllib__IORedirection_t.java','./SWIGTYPE_p_FILE.java','./BloomFilter.java','./SWIGTYPE_p_unsigned_long_long.java','./SeedNtHash.java','./SeqReader.java','./KmerBloomFilter.java','./SWIGTYPE_p_p_unsigned_long_long.java','./SeqWriter.java','./SWIGTYPE_p_p_btllib__Indexlr__Minimizer.java','./SWIGTYPE_p_std__arrayT_int_2_t.java','./SWIGTYPE_p_std__vectorT_btllib__Indexlr__Minimizer_t.java','./SWIGTYPE_p_std__vectorT_SpacedSeed_t.java','./SeqReaderSamModule.java','./SWIGTYPE_p_btllib__IORedirection.java','./SeqReaderFastaModule.java','./SWIGTYPE_p_int.java','./SWIGTYPE_p_p_FILE.java','./ProcessPipelineInternal.java','./NtHash.java','./SWIGTYPE_p_std__shared_ptrT_cpptoml__table_t.java','./SWIGTYPE_p_mode_t.java','./SWIGTYPE_p_btllib__CString.java','./SeqReaderMultilineFastaModule.java','./Datatype.java','./SWIGTYPE_p_ssize_t.java','./SWIGTYPE_p_std__mutex.java','./SeqReaderMultilineFastqModule.java','./SWIGTYPE_p_unsigned_char.java','./Indexlr.java','./SeqReaderGfa2Module.java','./SWIGTYPE_p_std__vectorT_std__string_t.java','./SWIGTYPE_p_std__ios.java','./DataStream.java','./SeedBloomFilter.java','./DataSink.java']
 install_data(java_files, install_dir : 'java')

RResolver/btllib/extras/python/btllib.py

@@ -92,5 +92,6 @@ class _SwigNonDynamicMeta(type):
 
 
 
+