Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / clustal / progress.c

diff --git a/binaries/src/clustalo/src/clustal/progress.c b/binaries/src/clustalo/src/clustal/progress.c
new file mode 100644 (file)
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+++ b/binaries/src/clustalo/src/clustal/progress.c
@@ -0,0 +1,177 @@
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4;  indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ *  RCS $Id: progress.c 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include "util.h"
+#include "log.h"
+#include "progress.h"
+
+#define LOGLEVEL_THRESHOLD LOG_INFO
+
+/**
+ * @brief Allocates a new progress structure and initialises its members.
+ * Free with FreeProgress()
+ *
+ * @note Starts the internal stopwatch immediatly!
+ *
+ * @see FreeProgress()
+ *
+ * @param[out] pprProgress
+ * Pointer pointer to progress structure. Progress structure will be
+ * allocated here. 
+ * @param[in] prFile
+ * Where to log messages to
+ * @param[in] pcPrefix
+ * What prefix to use for messages
+ * @param[in] bPrintCR
+ * If TRUE carriage return instead of newline will be printed between log messages
+ */    
+void
+NewProgress(progress_t **pprProgress, FILE *prFile,
+            char *pcPrefix, bool bPrintCR)
+{
+    assert(NULL!=pprProgress);
+    assert(NULL!=prFile);
+    assert(NULL!=pcPrefix);
+    
+    (*pprProgress) = (progress_t *) CKMALLOC(1*sizeof(progress_t));
+    (*pprProgress)->prFile = prFile;
+    (*pprProgress)->bPrintCR = bPrintCR;    
+    (*pprProgress)->pcPrefix = CkStrdup(pcPrefix);
+    strcpy((*pprProgress)->pcLastLogMsg, "\0");
+    (*pprProgress)->prStopwatch = StopwatchCreate();
+    StopwatchZero((*pprProgress)->prStopwatch);
+    StopwatchStart((*pprProgress)->prStopwatch);
+    
+    return; 
+}
+/***   end: NewProgress()   ***/
+
+
+
+/**
+ * @brief Frees progress structure and its members
+ *
+ * @param[out] pprProgress
+ * Pointer pointer to progress structure
+ *
+ * @see NewProgress()
+ * 
+ */    
+void
+FreeProgress(progress_t **pprProgress)
+{
+    (*pprProgress)->prFile = NULL;
+    CKFREE((*pprProgress)->pcPrefix);
+    StopwatchFree((*pprProgress)->prStopwatch);
+
+    CKFREE(*pprProgress);
+    return; 
+}
+/***   end: FreeProgress()   ***/
+
+
+
+
+/**
+ * @brief Prints a progress update (and a carriage return)
+ *
+ * @param[in] prProgress
+ * Pointer to the progress structure
+ * @param[in] iStep
+ * Current step number
+ * @param[in] iTotalSteps
+ * Total step number
+ * @param[in] bForceOutput
+ * If percentage hasn't changed output is normally supressed
+ * normally. Output can be forced with this flag.
+ *
+ */    
+void
+ProgressLog(progress_t *prProgress, 
+            unsigned long int iStep, unsigned long int iTotalSteps, 
+            bool bForceOutput)
+{
+    char pcLogMsg[1024];
+    assert(0!=iTotalSteps);
+    
+    if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) {
+        return;
+    }
+    
+    (void) snprintf(pcLogMsg, sizeof(pcLogMsg), "%s: %lu %%",
+                    prProgress->pcPrefix, (unsigned long int)(iStep/(float)iTotalSteps*100.0));
+
+    if (! bForceOutput) {
+        /* Skip logging, if we've just logged the same message */
+        if (STR_EQ(pcLogMsg, prProgress->pcLastLogMsg)) {
+            return;
+        }
+    }
+
+    strncpy(prProgress->pcLastLogMsg, pcLogMsg,
+            sizeof(prProgress->pcLastLogMsg));
+    
+    fprintf(prProgress->prFile, "%s (%lu out of %lu)", pcLogMsg, iStep, iTotalSteps);
+    if (prProgress->bPrintCR) {
+        fprintf(prProgress->prFile, "\r");
+    } else {
+        fprintf(prProgress->prFile, "\n");
+
+    }
+    (void) fflush(prProgress->prFile);
+
+    return; 
+}
+/***   end: ProgressLog()   ***/
+
+
+/**
+ * @brief Finishes progress output by printing the elapsed time
+ *
+ * @param[in] prProgress
+ * Pointer to the progress structure
+ *
+ */    
+void
+ProgressDone(progress_t *prProgress)
+{
+    char pcBuf[1024];
+
+    if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) {
+        return;
+    }
+
+    (void) snprintf(pcBuf, sizeof(pcBuf), "%s done. CPU time: ", 
+                    prProgress->pcPrefix);
+    StopwatchStop(prProgress->prStopwatch);
+    StopwatchDisplay(prProgress->prFile, pcBuf, prProgress->prStopwatch);
+    (void) fflush(prProgress->prFile);
+
+    return; 
+}
+/***   end: ProgressDone()   ***/