X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FSamHeader.cpp;h=5de2abcd9006d6eb86693973c416b0a61b9b2998;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=7a69162027a07fca6a2aa641048481e3d6245498;hpb=8c80d760637f8df39262683cd2570f0589423d36;p=bamtools.git

diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp
index 7a69162..5de2abc 100644
--- a/src/api/SamHeader.cpp
+++ b/src/api/SamHeader.cpp
@@ -1,17 +1,18 @@
 // ***************************************************************************
 // SamHeader.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides direct read/write access to the SAM header data fields.
 // ***************************************************************************
 
-#include <api/SamHeader.h>
-#include <api/internal/SamFormatParser_p.h>
-#include <api/internal/SamFormatPrinter_p.h>
-#include <api/internal/SamHeaderValidator_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/SamFormatParser_p.h"
+#include "api/internal/SamFormatPrinter_p.h"
+#include "api/internal/SamHeaderValidator_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 using namespace std;
@@ -21,10 +22,12 @@ using namespace std;
 
     Provides direct read/write access to the SAM header data fields.
 
-    \sa http://samtools.sourceforge.net/SAM-1.3.pdf
+    \sa \samSpecURL
 */
 /*! \var SamHeader::Version
     \brief corresponds to \@HD VN:\<Version\>
+
+    Required for valid SAM header, if \@HD record is present.
 */
 /*! \var SamHeader::SortOrder
     \brief corresponds to \@HD SO:\<SortOrder\>
@@ -40,14 +43,9 @@ using namespace std;
     \brief corresponds to \@RG entries
     \sa SamReadGroup, SamReadGroupDictionary
 */
-/*! \var SamHeader::ProgramName
-    \brief corresponds to \@PG ID:\<ProgramName\>
-*/
-/*! \var SamHeader::ProgramVersion
-    \brief corresponds to \@PG VN:\<ProgramVersion\>
-*/
-/*! \var SamHeader::ProgramCommandLine
-    \brief corresponds to \@PG CL:\<ProgramCommandLine\>
+/*! \var SamHeader::Programs
+    \brief corresponds to \@PG entries
+    \sa SamProgram, SamProgramChain
 */
 /*! \var SamHeader::Comments
     \brief corresponds to \@CO entries
@@ -58,14 +56,10 @@ using namespace std;
 */
 SamHeader::SamHeader(const std::string& headerText)
     : Version("")
-    , SortOrder("")
+    , SortOrder(Constants::SAM_HD_SORTORDER_UNKNOWN)
     , GroupOrder("")
-    , ProgramName("")
-    , ProgramVersion("")
-    , ProgramCommandLine("")
 {
-    SamFormatParser parser(*this);
-    parser.Parse(headerText);
+    SetHeaderText(headerText);
 }
 
 /*! \fn SamHeader::SamHeader(const SamHeader& other)
@@ -77,9 +71,7 @@ SamHeader::SamHeader(const SamHeader& other)
     , GroupOrder(other.GroupOrder)
     , Sequences(other.Sequences)
     , ReadGroups(other.ReadGroups)
-    , ProgramName(other.ProgramName)
-    , ProgramVersion(other.ProgramVersion)
-    , ProgramCommandLine(other.ProgramCommandLine)
+    , Programs(other.Programs)
 { }
 
 /*! \fn SamHeader::~SamHeader(void)
@@ -91,15 +83,37 @@ SamHeader::~SamHeader(void) { }
     \brief Clears all header contents.
 */
 void SamHeader::Clear(void) {
+
+    // clear SAM header components
     Version.clear();
     SortOrder.clear();
     GroupOrder.clear();
     Sequences.Clear();
     ReadGroups.Clear();
-    ProgramName.clear();
-    ProgramVersion.clear();
-    ProgramCommandLine.clear();
+    Programs.Clear();
     Comments.clear();
+
+    // clear error string
+    m_errorString.clear();
+}
+
+/*! \fn std::string SamHeader::GetErrorString(void) const
+    \brief Returns a human-readable description of the last error that occurred
+
+    This method allows elimination of STDERR pollution. Developers of client code
+    may choose how the messages are displayed to the user, if at all.
+
+    \return error description
+*/
+std::string SamHeader::GetErrorString(void) const {
+    return m_errorString;
+}
+
+/*! \fn bool SamHeader::HasError(void) const
+    \brief Returns \c true if header encountered an error
+*/
+bool SamHeader::HasError(void) const {
+    return (!m_errorString.empty());
 }
 
 /*! \fn bool SamHeader::HasVersion(void) const
@@ -137,25 +151,11 @@ bool SamHeader::HasReadGroups(void) const {
     return (!ReadGroups.IsEmpty());
 }
 
-/*! \fn bool SamHeader::HasProgramName(void) const
-    \brief Returns \c true if header contains \@PG ID:\<ProgramName\>
+/*! \fn bool SamHeader::HasPrograms(void) const
+    \brief Returns \c true if header contains any \@PG entries
 */
-bool SamHeader::HasProgramName(void) const {
-    return (!ProgramName.empty());
-}
-
-/*! \fn bool SamHeader::HasProgramVersion(void) const
-    \brief Returns \c true if header contains \@PG VN:\<ProgramVersion\>
-*/
-bool SamHeader::HasProgramVersion(void) const {
-    return (!ProgramVersion.empty());
-}
-
-/*! \fn bool SamHeader::HasProgramCommandLine(void) const
-    \brief Returns \c true if header contains \@PG CL:\<ProgramCommandLine\>
-*/
-bool SamHeader::HasProgramCommandLine(void) const {
-    return (!ProgramCommandLine.empty());
+bool SamHeader::HasPrograms(void) const {
+    return (!Programs.IsEmpty());
 }
 
 /*! \fn bool SamHeader::HasComments(void) const
@@ -167,27 +167,58 @@ bool SamHeader::HasComments(void) const {
 
 /*! \fn bool SamHeader::IsValid(bool verbose = false) const
     \brief Checks header contents for required data and proper formatting.
-    \param verbose If set to true, validation errors & warnings will be printed to stderr.
-                   Otherwise, output is suppressed and only validation check occurs.
+
+    \param[in] verbose If set to true, validation errors & warnings will be printed to stderr.
+                       Otherwise, messages are available through SamHeader::GetErrorString().
     \return \c true if SAM header is well-formed
 */
 bool SamHeader::IsValid(bool verbose) const {
+
     SamHeaderValidator validator(*this);
-    return validator.Validate(verbose);
+
+    // if SAM header is valid, return success
+    if ( validator.Validate() )
+        return true;
+
+    // otherwiser
+    else {
+
+        // print messages to stderr
+        if ( verbose )
+            validator.PrintMessages(std::cerr);
+
+        // or catch in local error string
+        else {
+            stringstream errorStream("");
+            validator.PrintMessages(errorStream);
+            m_errorString = errorStream.str();
+        }
+        return false;
+    }
 }
 
 /*! \fn void SamHeader::SetHeaderText(const std::string& headerText)
     \brief Replaces header contents with \a headerText.
-    \param headerText SAM formatted-text that will be parsed into data fields
+
+    \param[in] headerText SAM formatted-text that will be parsed into data fields
 */
 void SamHeader::SetHeaderText(const std::string& headerText) {
 
     // clear prior data
     Clear();
 
-    // parse header text into data
-    SamFormatParser parser(*this);
-    parser.Parse(headerText);
+    try {
+        SamFormatParser parser(*this);
+        parser.Parse(headerText);
+    } catch ( BamException& e ) {
+
+        // clear anything parsed so far
+        // no telling what's valid and what's partially parsed
+        Clear();
+
+        // set error string
+        m_errorString = e.what();
+    }
 }
 
 /*! \fn std::string SamHeader::ToString(void) const