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[Sashimi-commit] SF.net SVN: sashimi:[5943] branches/4-6/trans_proteomic_pipeline/extern/ xtandem/src_tpp
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From: <sla...@us...> - 2012-09-24 16:56:51
|
Revision: 5943
http://sashimi.svn.sourceforge.net/sashimi/?rev=5943&view=rev
Author: slagelwa
Date: 2012-09-24 16:56:45 +0000 (Mon, 24 Sep 2012)
Log Message:
-----------
Fix a few free pointer vs array reported by valgrind that have
the potential of memory leaks/heap corruption on some platforms.
Modified Paths:
--------------
branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mmotif.h
branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mscore.cpp
branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/msequtilities.cpp
Modified: branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mmotif.h
===================================================================
--- branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mmotif.h 2012-09-18 09:56:48 UTC (rev 5942)
+++ branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mmotif.h 2012-09-24 16:56:45 UTC (rev 5943)
@@ -366,7 +366,7 @@
}
a++;
}
- delete pOut;
+ delete []pOut;
return true;
}
Modified: branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mscore.cpp
===================================================================
--- branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mscore.cpp 2012-09-18 09:56:48 UTC (rev 5942)
+++ branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/mscore.cpp 2012-09-24 16:56:45 UTC (rev 5943)
@@ -1,6 +1,6 @@
/*
Copyright (C) 2003-2004 Ronald C Beavis, all rights reserved
- X! tandem
+ X! tandem
This software is a component of the X! proteomics software
development project
@@ -10,122 +10,122 @@
Preamble
The intent of this document is to state the conditions under which a
-Package may be copied, such that the Copyright Holder maintains some
-semblance of artistic control over the development of the package,
-while giving the users of the package the right to use and distribute
-the Package in a more-or-less customary fashion, plus the right to
-make reasonable modifications.
+Package may be copied, such that the Copyright Holder maintains some
+semblance of artistic control over the development of the package,
+while giving the users of the package the right to use and distribute
+the Package in a more-or-less customary fashion, plus the right to
+make reasonable modifications.
Definitions
-"Package" refers to the collection of files distributed by the Copyright
- Holder, and derivatives of that collection of files created through
- textual modification.
+"Package" refers to the collection of files distributed by the Copyright
+ Holder, and derivatives of that collection of files created through
+ textual modification.
-"Standard Version" refers to such a Package if it has not been modified,
- or has been modified in accordance with the wishes of the Copyright
- Holder as specified below.
+"Standard Version" refers to such a Package if it has not been modified,
+ or has been modified in accordance with the wishes of the Copyright
+ Holder as specified below.
-"Copyright Holder" is whoever is named in the copyright or copyrights
- for the package.
+"Copyright Holder" is whoever is named in the copyright or copyrights
+ for the package.
-"You" is you, if you're thinking about copying or distributing this Package.
+"You" is you, if you're thinking about copying or distributing this Package.
-"Reasonable copying fee" is whatever you can justify on the basis of
- media cost, duplication charges, time of people involved, and so on.
- (You will not be required to justify it to the Copyright Holder, but
- only to the computing community at large as a market that must bear
- the fee.)
+"Reasonable copying fee" is whatever you can justify on the basis of
+ media cost, duplication charges, time of people involved, and so on.
+ (You will not be required to justify it to the Copyright Holder, but
+ only to the computing community at large as a market that must bear
+ the fee.)
-"Freely Available" means that no fee is charged for the item itself,
- though there may be fees involved in handling the item. It also means
+"Freely Available" means that no fee is charged for the item itself,
+ though there may be fees involved in handling the item. It also means
that recipients of the item may redistribute it under the same
- conditions they received it.
+ conditions they received it.
-1. You may make and give away verbatim copies of the source form of the
-Standard Version of this Package without restriction, provided that
-you duplicate all of the original copyright notices and associated
-disclaimers.
+1. You may make and give away verbatim copies of the source form of the
+Standard Version of this Package without restriction, provided that
+you duplicate all of the original copyright notices and associated
+disclaimers.
-2. You may apply bug fixes, portability fixes and other modifications
-derived from the Public Domain or from the Copyright Holder. A
-Package modified in such a way shall still be considered the Standard
-Version.
+2. You may apply bug fixes, portability fixes and other modifications
+derived from the Public Domain or from the Copyright Holder. A
+Package modified in such a way shall still be considered the Standard
+Version.
-3. You may otherwise modify your copy of this Package in any way, provided
-that you insert a prominent notice in each changed file stating how and
-when you changed that file, and provided that you do at least ONE of the
-following:
+3. You may otherwise modify your copy of this Package in any way, provided
+that you insert a prominent notice in each changed file stating how and
+when you changed that file, and provided that you do at least ONE of the
+following:
-a. place your modifications in the Public Domain or otherwise make them
- Freely Available, such as by posting said modifications to Usenet
- or an equivalent medium, or placing the modifications on a major
- archive site such as uunet.uu.net, or by allowing the Copyright Holder
- to include your modifications in the Standard Version of the Package.
-b. use the modified Package only within your corporation or organization.
-c. rename any non-standard executables so the names do not conflict
- with standard executables, which must also be provided, and provide
- a separate manual page for each non-standard executable that clearly
- documents how it differs from the Standard Version.
-d. make other distribution arrangements with the Copyright Holder.
+a. place your modifications in the Public Domain or otherwise make them
+ Freely Available, such as by posting said modifications to Usenet
+ or an equivalent medium, or placing the modifications on a major
+ archive site such as uunet.uu.net, or by allowing the Copyright Holder
+ to include your modifications in the Standard Version of the Package.
+b. use the modified Package only within your corporation or organization.
+c. rename any non-standard executables so the names do not conflict
+ with standard executables, which must also be provided, and provide
+ a separate manual page for each non-standard executable that clearly
+ documents how it differs from the Standard Version.
+d. make other distribution arrangements with the Copyright Holder.
-4. You may distribute the programs of this Package in object code or
-executable form, provided that you do at least ONE of the following:
+4. You may distribute the programs of this Package in object code or
+executable form, provided that you do at least ONE of the following:
-a. distribute a Standard Version of the executables and library files,
- together with instructions (in the manual page or equivalent) on
- where to get the Standard Version.
-b. accompany the distribution with the machine-readable source of the
- Package with your modifications.
-c. give non-standard executables non-standard names, and clearly
- document the differences in manual pages (or equivalent), together
- with instructions on where to get the Standard Version.
-d. make other distribution arrangements with the Copyright Holder.
+a. distribute a Standard Version of the executables and library files,
+ together with instructions (in the manual page or equivalent) on
+ where to get the Standard Version.
+b. accompany the distribution with the machine-readable source of the
+ Package with your modifications.
+c. give non-standard executables non-standard names, and clearly
+ document the differences in manual pages (or equivalent), together
+ with instructions on where to get the Standard Version.
+d. make other distribution arrangements with the Copyright Holder.
-5. You may charge a reasonable copying fee for any distribution of
-this Package. You may charge any fee you choose for support of
-this Package. You may not charge a fee for this Package itself.
-However, you may distribute this Package in aggregate with other
-(possibly commercial) programs as part of a larger (possibly
+5. You may charge a reasonable copying fee for any distribution of
+this Package. You may charge any fee you choose for support of
+this Package. You may not charge a fee for this Package itself.
+However, you may distribute this Package in aggregate with other
+(possibly commercial) programs as part of a larger (possibly
commercial) software distribution provided that you do not a
-dvertise this Package as a product of your own. You may embed this
-Package's interpreter within an executable of yours (by linking);
-this shall be construed as a mere form of aggregation, provided that
-the complete Standard Version of the interpreter is so embedded.
+dvertise this Package as a product of your own. You may embed this
+Package's interpreter within an executable of yours (by linking);
+this shall be construed as a mere form of aggregation, provided that
+the complete Standard Version of the interpreter is so embedded.
-6. The scripts and library files supplied as input to or produced as
-output from the programs of this Package do not automatically fall
-under the copyright of this Package, but belong to whomever generated
-them, and may be sold commercially, and may be aggregated with this
-Package. If such scripts or library files are aggregated with this
-Package via the so-called "undump" or "unexec" methods of producing
-a binary executable image, then distribution of such an image shall
-neither be construed as a distribution of this Package nor shall it
-fall under the restrictions of Paragraphs 3 and 4, provided that you
-do not represent such an executable image as a Standard Version of
-this Package.
+6. The scripts and library files supplied as input to or produced as
+output from the programs of this Package do not automatically fall
+under the copyright of this Package, but belong to whomever generated
+them, and may be sold commercially, and may be aggregated with this
+Package. If such scripts or library files are aggregated with this
+Package via the so-called "undump" or "unexec" methods of producing
+a binary executable image, then distribution of such an image shall
+neither be construed as a distribution of this Package nor shall it
+fall under the restrictions of Paragraphs 3 and 4, provided that you
+do not represent such an executable image as a Standard Version of
+this Package.
-7. C subroutines (or comparably compiled subroutines in other languages)
-supplied by you and linked into this Package in order to emulate
-subroutines and variables of the language defined by this Package
-shall not be considered part of this Package, but are the equivalent
-of input as in Paragraph 6, provided these subroutines do not change
-the language in any way that would cause it to fail the regression
-tests for the language.
+7. C subroutines (or comparably compiled subroutines in other languages)
+supplied by you and linked into this Package in order to emulate
+subroutines and variables of the language defined by this Package
+shall not be considered part of this Package, but are the equivalent
+of input as in Paragraph 6, provided these subroutines do not change
+the language in any way that would cause it to fail the regression
+tests for the language.
-8. Aggregation of this Package with a commercial distribution is always
-permitted provided that the use of this Package is embedded; that is,
-when no overt attempt is made to make this Package's interfaces visible
-to the end user of the commercial distribution. Such use shall not be
-construed as a distribution of this Package.
+8. Aggregation of this Package with a commercial distribution is always
+permitted provided that the use of this Package is embedded; that is,
+when no overt attempt is made to make this Package's interfaces visible
+to the end user of the commercial distribution. Such use shall not be
+construed as a distribution of this Package.
-9. The name of the Copyright Holder may not be used to endorse or promote
-products derived from this software without specific prior written permission.
+9. The name of the Copyright Holder may not be used to endorse or promote
+products derived from this software without specific prior written permission.
-10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
-MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-The End
+The End
*/
// File version: 2003-08-01
@@ -159,7 +159,7 @@
*/
bool lessThanDetails(const mspectrumdetails &_l,const mspectrumdetails &_r)
{
- return _l.m_fL < _r.m_fL;
+ return _l.m_fL < _r.m_fL;
}
/*
* global less than operator for mi classes: to be used in sort operations to achieve
@@ -185,7 +185,7 @@
m_fParentErrPlus = 2.0;
m_fParentErrMinus = 2.0;
m_fErr = (float)0.45;
-
+
m_fWidth = 1.0;
m_lMaxCharge = 100;
m_dSeqMH = -1.0;
@@ -216,13 +216,13 @@
mscore::~mscore(void)
{
if(m_pfSeq != NULL)
- delete m_pfSeq;
+ delete[] m_pfSeq;
if(m_plSeq != NULL)
- delete m_plSeq;
+ delete[] m_plSeq;
if(m_pSeq != NULL)
delete[] m_pSeq;
if(m_plAA != NULL)
- delete m_plAA;
+ delete[] m_plAA;
}
bool mscore::set_mini(const bool _b)
@@ -290,7 +290,7 @@
* deal with protein N-terminus
*/
if(m_bIsN) {
- dValue += m_pSeqUtilFrag->m_fNT;
+ dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
@@ -335,7 +335,7 @@
a++;
}
/*
- * set the next integer mass value to 0: this marks the end of the array
+ * set the next integer mass value to 0: this marks the end of the array
*/
m_lCount = lCount;
m_plSeq[lCount] = 0;
@@ -356,7 +356,7 @@
* deal with protein N-terminus
*/
if(m_bIsN) {
- dValue += m_pSeqUtilFrag->m_fNT;
+ dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
@@ -428,7 +428,7 @@
* deal with protein N-terminus
*/
if(m_bIsN) {
- dValue += m_pSeqUtilFrag->m_fNT;
+ dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
@@ -500,7 +500,7 @@
* deal with protein C-teminus
*/
if(m_bIsC) {
- dValue += m_pSeqUtilFrag->m_fCT;
+ dValue += m_pSeqUtilFrag->m_fCT;
}
unsigned long lValue = 0;
/*
@@ -538,7 +538,7 @@
a--;
}
/*
- * set the next integer mass value to 0: this marks the end of the array
+ * set the next integer mass value to 0: this marks the end of the array
*/
m_lCount = lCount;
m_plSeq[lCount] = 0;
@@ -569,7 +569,7 @@
* deal with protein C-teminus
*/
if(m_bIsC) {
- dValue += m_pSeqUtilFrag->m_fCT;
+ dValue += m_pSeqUtilFrag->m_fCT;
}
unsigned long lCount = 0;
float fSub = 0.0;
@@ -624,7 +624,7 @@
a--;
}
/*
- * set the next integer mass value to 0: this marks the end of the array
+ * set the next integer mass value to 0: this marks the end of the array
*/
m_lCount = lCount;
m_plSeq[lCount] = 0;
@@ -656,7 +656,7 @@
* deal with protein C-teminus
*/
if(m_bIsC) {
- dValue += m_pSeqUtilFrag->m_fCT;
+ dValue += m_pSeqUtilFrag->m_fCT;
}
size_t tC = 0;
unsigned long lCount = 0;
@@ -693,7 +693,7 @@
a--;
}
/*
- * set the next integer mass value to 0: this marks the end of the array
+ * set the next integer mass value to 0: this marks the end of the array
*/
m_lCount = lCount;
m_plSeq[lCount] = 0;
@@ -750,7 +750,7 @@
}
/*
- * add_mi does the work necessary to set up an mspectrum object for modeling.
+ * add_mi does the work necessary to set up an mspectrum object for modeling.
* - a copy of the mspectrum object is added to m_vSpec
* - an entry in the m_State object is made for the parent ion M+H
* once an mspectrum has been added, the original mspectrum is no longer
@@ -832,7 +832,7 @@
return set_seq(_s,_n,_c,_l,_f);
}
/*
- * copy the new part of the sequence into m_pSeq
+ * copy the new part of the sequence into m_pSeq
*/
strcpy(m_pSeq + lOldLength,_s + lOldLength);
unsigned long a = lOldLength;
@@ -878,7 +878,7 @@
if(m_bIsC)
m_dSeqMH += m_seqUtil.m_fCT;
/*
- * update the mstate object
+ * update the mstate object
*/
m_State.m_dSeqMHS = m_dSeqMH;
m_fMinMass = (float)m_dSeqMH;
@@ -955,7 +955,7 @@
return false;
}
/*
- * get_aa is used to check the current sequence and determine how many of
+ * get_aa is used to check the current sequence and determine how many of
* the residues correspond to modification sites. this method is not used
* by mscore: check mprocess to see an example of how it is used to create
* a list of modified residues in a domain
@@ -1012,7 +1012,7 @@
}
}
a++;
- }
+ }
if(m_seqUtil.m_bSequenceMods) {
SMap::iterator itValue = m_seqUtil.m_mapMods.begin();
SMap::const_iterator itEnd = m_seqUtil.m_mapMods.end();
@@ -1146,7 +1146,7 @@
/*
* load_next is used access the potential sequence modification state machine.
* it runs the state machine until either:
- * - a modified sequence that has a mass that is within error of
+ * - a modified sequence that has a mass that is within error of
* one of the mspectrum objects has been found, or
* - the last of the modified sequences has been returned
* it returns true if there are more sequences to consider.
@@ -1417,7 +1417,7 @@
/*
* load_state is used access the potential sequence modification state machine.
* it runs the state machine until either:
- * - a modified sequence that has a mass that is within error of
+ * - a modified sequence that has a mass that is within error of
* one of the mspectrum objects has been found, or
* - the last of the modified sequences has been returned
* it returns true if there are more sequences to consider.
@@ -1592,7 +1592,7 @@
{
unsigned long pos = m_State.m_piMods[i];
*(m_State.m_ppModsS[pos]) += 32;
- m_dSeqMH += m_seqUtil.m_pdAaMod[*(m_State.m_ppModsS[pos])];
+ m_dSeqMH += m_seqUtil.m_pdAaMod[*(m_State.m_ppModsS[pos])];
} */
m_plAA['s'] = 0;
m_plAA['t'] = 0;
@@ -1853,9 +1853,9 @@
m_lSeqLength = _l;
if(m_lSeqLength >= m_lSize-1) {
if(m_pfSeq != NULL)
- delete m_pfSeq;
+ delete[] m_pfSeq;
if(m_plSeq != NULL)
- delete m_plSeq;
+ delete[] m_plSeq;
if(m_pSeq != NULL)
delete[] m_pSeq;
m_lSize = m_lSeqLength + 16;
Modified: branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/msequtilities.cpp
===================================================================
--- branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/msequtilities.cpp 2012-09-18 09:56:48 UTC (rev 5942)
+++ branches/4-6/trans_proteomic_pipeline/extern/xtandem/src_tpp/msequtilities.cpp 2012-09-24 16:56:45 UTC (rev 5943)
@@ -530,7 +530,7 @@
}
pValue++;
}
- delete pString;
+ delete[] pString;
return true;
}
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