[med-svn] [Git][med-team/ugene][upstream] New upstream version 1.31.1+dfsg1
Andreas Tille
gitlab at salsa.debian.org
Fri Feb 1 09:17:16 GMT 2019
Andreas Tille pushed to branch upstream at Debian Med / ugene
Commits:
b00eb8f9 by Andreas Tille at 2019-02-01T08:26:59Z
New upstream version 1.31.1+dfsg1
- - - - -
16 changed files:
- − src/plugins_3rdparty/psipred/datafiles/weights_p2.dat
- − src/plugins_3rdparty/psipred/datafiles/weights_s.dat
- − src/plugins_3rdparty/psipred/datafiles/weights_s.dat2
- − src/plugins_3rdparty/psipred/datafiles/weights_s.dat3
- − src/plugins_3rdparty/psipred/psipred.license
- − src/plugins_3rdparty/psipred/src/LICENSE
- − src/plugins_3rdparty/psipred/src/seq2mtx.cpp
- − src/plugins_3rdparty/psipred/src/ssdefs.h
- − src/plugins_3rdparty/psipred/src/sspred_avpred.cpp
- − src/plugins_3rdparty/psipred/src/sspred_avpred.h
- − src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp
- − src/plugins_3rdparty/psipred/src/sspred_hmulti.h
- − src/plugins_3rdparty/psipred/src/sspred_net.h
- − src/plugins_3rdparty/psipred/src/sspred_net2.h
- − src/plugins_3rdparty/psipred/src/sspred_utils.cpp
- − src/plugins_3rdparty/psipred/src/sspred_utils.h
Changes:
=====================================
src/plugins_3rdparty/psipred/datafiles/weights_p2.dat deleted
=====================================
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@@ -1,74 +0,0 @@
- PSIPRED3 - PROTEIN SECONDARY STRUCTURE PREDICTION PROGRAM BY D.T.JONES
-
- GENERAL LICENSE & CONFIDENTIALITY AGREEMENT
-
-In regard to the protein structure prediction program (PSIPRED3)
-herewith (the Software) the copyright and other intellectual property
-rights to which belong to the Author(s).
-
-Any user (the User) of the program undertakes to the Copyright holder that he
-or she shall be bound by the following terms and conditions:-
-
-1. The User will receive the Software and any related documentation in
-confidence and will not use the same except for the purpose of their own
-research. The Software will be used only by such of the User's officers or
-employees to whom it must reasonably be communicated to enable them to
-undertake their research and who agree to be bound by the same confidence.
-The User shall procure and enforce such agreement from his or her staff for
-the benefit of the Copyright holder.
-
-2. The publication of research using the Software must include an
-appropriate citation to the method:
-
-Jones, D.T. (1999) Protein secondary structure prediction based on
-position-specific scoring matrices. J. Mol. Biol. 292:195-202.
-
-3. All forms of the Software will be kept in a reasonably secure place to
-prevent unauthorised access.
-
-4. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking maintained)
-with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights
-Reserved.".
-
-5. The Software may be modified, but any changes made shall be communicated
-to the Author(s) and made freely available.
-
-6. The Software may not be sold as a standalone package, or incorporated into
-a commercial software package without the written permission of the Copyright
-holder. The Software may be used freely for individual academic or commercial
-research. The Software may also be made freely available for training or
-teaching purposes.
-
-7. The results produced by the Software may not be incorporated into any
-data banks or databases which are subject to the payment of access or
-license fees without the written permission of the Copyright holder.
-
-8. The Software may be made available to users over a local network or
-wide area network (including the Internet), but only if access is granted
-free of charge to all authorised users. Incorporation of the Software into
-a commercial Web site or other fee paying service is not allowed without
-the written permission of the Copyright holder. If PSIPRED results are
-returned to the user via such a network service, then a suitable
-acknowledgement of the PSIPRED method must be returned somewhere in the
-output text.
-
-9. The confidentiality obligation in paragraph one shall not apply:
-
- (i) to information and data known to the User at the time of
- receipt hereunder (as evidenced by its written records);
-
- (ii) to information and data which was at the time of receipt in the
- public domain or thereafter becomes so through no wrongful act of
- the User;
-
- (iii) to information and data which the User receives from a third
- party not in breach of any obligation of confidentiality owed to
- the Author(s).
-
-10. The User understands that the Software is supplied "as is". No warranty
- as to its fitness or suitability for any purpose whatsoever is made or
- implied. In no event shall the Author(s) or Copyright holder be held
- responsible for any direct or indirect damages arising through the use
- of the Software.
-
=====================================
src/plugins_3rdparty/psipred/src/LICENSE deleted
=====================================
@@ -1,89 +0,0 @@
-PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE
-ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS
-AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES
-NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: dtj at cs.ucl.ac.uk
-
-* NOTE RECENT CHANGES TO PARAGRAPH 8 *
-
-
-
- PSIPRED2 - PROTEIN SECONDARY STRUCTURE PREDICTION PROGRAM BY D.T.JONES
- ----------------------------------------------------------------------
-
- GENERAL LICENSE &
- -----------------
-
- CONFIDENTIALITY AGREEMENT
- -------------------------
-
-
-
-In regard to the protein structure prediction program (PSIPRED2)
-herewith (the Software) the copyright and other intellectual property
-rights to which belong to the Author(s).
-
-Any user (the User) of the program undertakes to the Copyright holder that he
-or she shall be bound by the following terms and conditions:-
-
-1. The User will receive the Software and any related documentation in
-confidence and will not use the same except for the purpose of their own
-research. The Software will be used only by such of the User's officers or
-employees to whom it must reasonably be communicated to enable them to
-undertake their research and who agree to be bound by the same confidence.
-The User shall procure and enforce such agreement from his or her staff for
-the benefit of the Copyright holder.
-
-2. The publication of research using the Software must include an
-appropriate citation to the method:
-
-Jones, D.T. (1999) Protein secondary structure prediction based on
-position-specific scoring matrices. J. Mol. Biol. 292:195-202.
-
-3. All forms of the Software will be kept in a reasonably secure place to
-prevent unauthorised access.
-
-4. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking maintained)
-with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights
-Reserved.".
-
-5. The Software may be modified, but any changes made shall be communicated
-to the Author(s) and made freely available.
-
-6. The Software may not be sold as a standalone package, or incorporated into
-a commercial software package without the written permission of the Copyright
-holder. The Software may be used freely for individual academic or commercial
-research. The Software may also be made freely available for training or
-teaching purposes.
-
-7. The results produced by the Software may not be incorporated into any
-data banks or databases which are subject to the payment of access or
-license fees without the written permission of the Copyright holder.
-
-8. The Software may be made available to users over a local network or
-wide area network (including the Internet), but only if access is granted
-free of charge to all authorised users. Incorporation of the Software into
-a commercial Web site or other fee paying service is not allowed without
-the written permission of the Copyright holder. If PSIPRED results are
-returned to the user via such a network service, then a suitable
-acknowledgement of the PSIPRED method must be returned somewhere in the
-output text.
-
-9. The confidentiality obligation in paragraph one shall not apply:
-
- (i) to information and data known to the User at the time of
- receipt hereunder (as evidenced by its written records);
-
- (ii) to information and data which was at the time of receipt in the
- public domain or thereafter becomes so through no wrongful act of
- the User;
-
- (iii) to information and data which the User receives from a third
- party not in breach of any obligation of confidentiality owed to
- the Author(s).
-
-10. The User understands that the Software is supplied "as is". No warranty
- as to its fitness or suitability for any purpose whatsoever is made or
- implied. In no event shall the Author(s) or Copyright holder be held
- responsible for any direct or indirect damages arising through the use
- of the Software.
=====================================
src/plugins_3rdparty/psipred/src/seq2mtx.cpp deleted
=====================================
@@ -1,146 +0,0 @@
-/* seq2mtx - convert single sequence to pseudo IMPALA mtx file */
-
-/* Copyright (C) 2000 D.T. Jones */
-
-#include <QTemporaryFile>
-#include <QTextStream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <math.h>
-#include <string.h>
-
-#ifdef Q_OS_WIN
-#pragma warning(disable: 4996)
-#endif
-
-#include "sspred_utils.h"
-
-#define MAXSEQLEN 65536
-
-// #define FALSE 0
-// #define TRUE 1
-
-#define SQR(x) ((x)*(x))
-#define MIN(x,y) (((x)<(y))?(x):(y))
-#define MAX(x,y) (((x)>(y))?(x):(y))
-
-const char *rescodes = "ARNDCQEGHILKMFPSTWYVBZX";
-
-/* BLOSUM 62 */
-const short aamat[23][23] =
-{
- {4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0},
- {-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1},
- {-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1},
- {-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
- -3, -3, 4, 1, -1},
- {0, -3, -3, -3,10, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
- -2, -1, -3, -3, -2},
- {-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2,
- -1, -2, 0, 3, -1},
- {-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3,
- -2, -2, 1, 4, -1},
- {0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
- -3, -3, -1, -2, -1},
- {-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
- 2, -3, 0, 0, -1},
- {-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
- -1, 3, -3, -3, -1},
- {-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
- -1, 1, -4, -3, -1},
- {-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
- -2, -2, 0, 1, -1},
- {-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
- -1, 1, -3, -1, -1},
- {-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
- 3, -1, -3, -3, -1},
- {-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4,
- -3, -2, -2, -1, -2},
- {1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3,
- -2, -2, 0, 0, 0},
- {0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
- -2, 0, -1, -1, 0},
- {-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11,
- 2, -3, -4, -3, -2},
- {-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
- 7, -1, -3, -2, -1},
- {0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
- -1, 4, -3, -2, -1},
- {-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
- -3, -3, 4, 1, -1},
- {-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3,
- -2, -2, 1, 4, -1},
- {0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
- -1, -1, -1, -1, 4}
-};
-
-int seq2mtx(const char* seq, int seqlen, const char* outFileName)
-{
- int i, j;
- const char *ncbicodes = "XAXCDEFGHIKLMNPQRSTVWXYXXX";
-
- if (seqlen < 5 || seqlen >= MAXSEQLEN)
- fail("Sequence length error!");
-
-
- FILE* pFile = fopen( outFileName, "w" );
- if (!pFile)
- {
- fail("open file for writing failed");
- }
-
- fprintf(pFile, "%d\n", seqlen);
-
- for (i=0; i<seqlen; i++)
- putc(seq[i], pFile);
-
- fprintf(pFile, "\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n");
-
- for (i=0; i<seqlen; i++)
- {
- for (j=0; j<26; j++)
- if (ncbicodes[j] != 'X')
- fprintf(pFile, "%d ", aamat[aanum(seq[i])][aanum(ncbicodes[j])]*100);
- else
- fprintf(pFile, "-32768 ");
- putc('\n', pFile);
- }
- fclose(pFile);
-
- return 0;
-}
-
-int seq2mtx( const char* seq, int seqlen, QTemporaryFile* tmpFile )
-{
- int i, j;
- const char *ncbicodes = "XAXCDEFGHIKLMNPQRSTVWXYXXX";
-
- if (seqlen < 5 || seqlen >= MAXSEQLEN)
- fail("Sequence length error!");
- tmpFile->open();
- QTextStream stream(tmpFile);
-
- stream << seqlen << '\n';
-
- for (i=0; i<seqlen; i++)
- stream << seq[i];
-
- stream << "\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n";
-
- for (i=0; i<seqlen; i++)
- {
- for (j=0; j<26; j++)
- if (ncbicodes[j] != 'X')
- stream << aamat[aanum(seq[i])][aanum(ncbicodes[j])]*100 << " ";
- //fprintf(pFile, "%d ", aamat[aanum(seq[i])][aanum(ncbicodes[j])]*100);
- else
- stream << "-32768 ";
- //fprintf(pFile, "-32768 ");
- stream << '\n';
- //putc('\n', pFile);
- }
-
- return 0;
-
-}
=====================================
src/plugins_3rdparty/psipred/src/ssdefs.h deleted
=====================================
@@ -1,14 +0,0 @@
-#define MAXSEQLEN 10000
-
-#define SQR(x) ((x)*(x))
-#define MAX(x,y) ((x)>(y)?(x):(y))
-#define MIN(x,y) ((x)<(y)?(x):(y))
-
-#define REAL float
-
-/* logistic 'squashing' function (output range +/- 1.0) */
-#define logistic(x) ((REAL)1.0 / ((REAL)1.0 + (REAL)exp(-(x))))
-
-
-
-
=====================================
src/plugins_3rdparty/psipred/src/sspred_avpred.cpp deleted
=====================================
@@ -1,305 +0,0 @@
-/* PSIPRED 2 - Neural Network Prediction of Secondary Structure */
-
-/* Copyright (C) 2000 David T. Jones - Created : January 2000 */
-/* Original Neural Network code Copyright (C) 1990 David T. Jones */
-
-/* Average Prediction Module */
-
-#include <QDir>
-#include <QFile>
-#include <QTemporaryFile>
-#include <QTextStream>
-#include <QString>
-#include <U2Core/AppContext.h>
-#include <U2Core/AppSettings.h>
-#include <U2Core/UserApplicationsSettings.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <ctype.h>
-#include <time.h>
-
-#ifdef Q_OS_WIN
-#pragma warning(disable: 4996)
-#endif
-
-#include "sspred_avpred.h"
-#include "sspred_utils.h"
-#include "sspred_net.h"
-
-
-//void *calloc(), *malloc();
-
-// char *wtfnm;
-//
-// int nwtsum, fwt_to[TOTAL], lwt_to[TOTAL];
-// float activation[TOTAL], bias[TOTAL], *weight[TOTAL];
-//
-// int profile[MAXSEQLEN][20];
-//
-// int seqlen;
-//
-// char seq[MAXSEQLEN];
-
-enum aacodes
-{
- ALA, ARG, ASN, ASP, CYS,
- GLN, GLU, GLY, HIS, ILE,
- LEU, LYS, MET, PHE, PRO,
- SER, THR, TRP, TYR, VAL,
- UNK
-};
-
-
-PsiPassOne::PsiPassOne(QTemporaryFile* matFile, const QStringList& weightFiles) : matrixFile(matFile), weightFileNames(weightFiles) {
-
- fwt_to = (int*) malloc(TOTAL*sizeof(int));
- lwt_to = (int*) malloc(TOTAL*sizeof(int));
- activation = (float*) malloc(TOTAL*sizeof(float));
- bias = (float*) malloc(TOTAL*sizeof(float));
- weight = (float**) malloc(TOTAL*sizeof(float*));
-
- profile = (int **)malloc(MAXSEQLEN * sizeof(int *));
- for (int i = 0; i < MAXSEQLEN; i++) {
- profile[i] = (int *)malloc(20 * sizeof(int));
- }
-}
-
-PsiPassOne::~PsiPassOne()
-{
-
- free(fwt_to);
- free(lwt_to);
- free(activation);
- free(bias);
- free(weight);
-
- for (int i = 0; i < MAXSEQLEN; i++) {
- delete profile[i];
- }
- delete profile;
-}
-
-void PsiPassOne::compute_output(void)
-{
- int i, j;
- float netinp;
-
- for (i = NUM_IN; i < TOTAL; i++)
- {
- netinp = bias[i];
-
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- netinp += activation[j] * weight[i][j];
-
- /* Trigger neuron */
- activation[i] = logistic(netinp);
- }
-}
-
-/*
-* load weights - load all link weights from a disk file
-*/
-void PsiPassOne::load_wts( const char *fname )
-{
- int i, j;
- double t;
-
- QFile weightFile(fname);
- if (!weightFile.open(QIODevice::ReadOnly)) {
- return;
- }
-
- QTextStream stream(&weightFile);
-
- /* Load input units to hidden layer weights */
- for (i = NUM_IN; i < NUM_IN + NUM_HID; i++)
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- {
- stream >> t;
- weight[i][j] = t;
- }
-
- /* Load hidden layer to output units weights */
- for (i = NUM_IN + NUM_HID; i < TOTAL; i++)
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- {
- stream >> t;
- weight[i][j] = t;
- }
-
- /* Load bias weights */
- for (j = NUM_IN; j < TOTAL; j++)
- {
- stream >> t;
- bias[j] = t;
- }
-}
-
-/* Initialize network */
-void PsiPassOne::init(void)
-{
- int i;
-
- for (i = NUM_IN; i < TOTAL; i++)
- if (!(weight[i] = (float*) calloc(TOTAL - NUM_OUT, sizeof(float))))
- fail("init: Out of Memory!");
-
- /* Connect input units to hidden layer */
- for (i = NUM_IN; i < NUM_IN + NUM_HID; i++)
- {
- fwt_to[i] = 0;
- lwt_to[i] = NUM_IN;
- }
-
- /* Connect hidden units to output layer */
- for (i = NUM_IN + NUM_HID; i < TOTAL; i++)
- {
- fwt_to[i] = NUM_IN;
- lwt_to[i] = NUM_IN + NUM_HID;
- }
-}
-
-
-/* Make 1st level prediction averaged over specified weight sets */
-void PsiPassOne::predict()
-{
- //int aa, i, j, k, n, winpos,ws;
- int aa, j, winpos;
- //char fname[80], predsst[MAXSEQLEN];
- char *predsst;
- //float avout[MAXSEQLEN][3], conf, confsum[MAXSEQLEN];
- float **avout, conf, *confsum;
-
- // Allocate buffers
- // TODO: not good, memory is allocated in small chunks for avout
- predsst = (char*) malloc(seqlen*sizeof(char));
- avout = (float**) malloc(seqlen*sizeof(float*));
- for (int i = 0; i < seqlen; ++i) {
- avout[i] = (float*) malloc(3*sizeof(float));
- }
- confsum = (float*) malloc(seqlen*sizeof(float));
-
-
-
- for (winpos = 0; winpos < seqlen; winpos++)
- avout[winpos][0] = avout[winpos][1] = avout[winpos][2] = confsum[winpos] = 0.0F;
-
- foreach (const QString& wfName, weightFileNames)
- {
- load_wts(qPrintable(wfName));
-
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- for (j = 0; j < NUM_IN; j++)
- activation[j] = 0.0;
- for (j = WINL; j <= WINR; j++)
- {
- if (j + winpos >= 0 && j + winpos < seqlen)
- for (aa=0; aa<20; aa++)
- activation[(j - WINL) * 21 + aa] = profile[j+winpos][aa]/1000.0;
- else
- activation[(j - WINL) * 21 + 20] = 1.0;
- }
-
- compute_output();
-
- conf = (2*MAX(MAX(activation[TOTAL - NUM_OUT], activation[TOTAL - NUM_OUT+1]), activation[TOTAL - NUM_OUT+2])-(activation[TOTAL - NUM_OUT]+activation[TOTAL - NUM_OUT+1]+activation[TOTAL - NUM_OUT+2])+MIN(MIN(activation[TOTAL - NUM_OUT], activation[TOTAL - NUM_OUT+1]), activation[TOTAL - NUM_OUT+2]));
-
- avout[winpos][0] += conf * activation[TOTAL - NUM_OUT];
- avout[winpos][1] += conf * activation[TOTAL - NUM_OUT+1];
- avout[winpos][2] += conf * activation[TOTAL - NUM_OUT+2];
- confsum[winpos] += conf;
- }
- }
-
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- avout[winpos][0] /= confsum[winpos];
- avout[winpos][1] /= confsum[winpos];
- avout[winpos][2] /= confsum[winpos];
- if (avout[winpos][0] >= MAX(avout[winpos][1], avout[winpos][2]))
- predsst[winpos] = 'C';
- else if (avout[winpos][2] >= MAX(avout[winpos][0], avout[winpos][1]))
- predsst[winpos] = 'E';
- else
- predsst[winpos] = 'H';
- }
- QString pFilePath = U2::AppContext::getAppSettings()->getUserAppsSettings()->getUserTemporaryDirPath() + QDir::separator() + "output.ss";
- FILE* pFile = fopen(pFilePath.toLatin1().constData(), "w");
- if (!pFile) {
- fail("failed opening file for writing");
- }
-
- for (winpos = 0; winpos < seqlen; winpos++)
- fprintf(pFile, "%4d %c %c %6.3f %6.3f %6.3f\n", winpos + 1, seq.constData()[winpos], predsst[winpos], avout[winpos][0], avout[winpos][1], avout[winpos][2]);
- fclose(pFile);
-
- // Deallocate buffers
- free(predsst);
- for (int i = 0; i < seqlen; ++i) {
- free(avout[i]);
- }
- free(avout);
- free(confsum);
-
-}
-
-#define BUFSIZE 256
-
-/* Read PSI AA frequency data */
-int PsiPassOne::getmtx()
-{
- int j, naa;
-
- QTextStream stream(matrixFile);
- qDebug("%s", qPrintable(matrixFile->fileName()));
-
- stream >> naa;
- if (naa == 0) {
- fail("Bad mtx file - no sequence length!");
- }
-
- if (naa > MAXSEQLEN)
- fail("Input sequence too long!");
-
- stream >> seq;
- if (seq.size() == 0)
- { fail("Bad mtx file - no sequence!");
- }
-
- while (!stream.atEnd())
- {
- QByteArray line;
- line = stream.readLine().toLatin1();
- char* buf = line.data();
- if (!strncmp(buf, "-32768 ", 7))
- {
- for (j=0; j<naa; j++)
- {
- if (sscanf(buf, "%*d%d%*d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%*d%d", &profile[j][ALA], &profile[j][CYS], &profile[j][ASP], &profile[j][GLU], &profile[j][PHE], &profile[j][GLY], &profile[j][HIS], &profile[j][ILE], &profile[j][LYS], &profile[j][LEU], &profile[j][MET], &profile[j][ASN], &profile[j][PRO], &profile[j][GLN], &profile[j][ARG], &profile[j][SER], &profile[j][THR], &profile[j][VAL], &profile[j][TRP], &profile[j][TYR]) != 20)
- fail("Bad mtx format!");
- line = stream.readLine().toLatin1();
- if (line.size() == 0)
- break;
- buf = line.data();
-
- }
- }
- }
-
- return naa;
-}
-
-int PsiPassOne::runPsiPass()
-{
-
- seqlen = getmtx();
-
- init();
-
- predict();
-
- return 0;
-}
=====================================
src/plugins_3rdparty/psipred/src/sspred_avpred.h deleted
=====================================
@@ -1,35 +0,0 @@
-#ifndef SSPRED_AVPRED_H
-#define SSPRED_AVPRED_H
-
-#include <QVector>
-#include <QByteArray>
-#include <QStringList>
-
-#include "ssdefs.h"
-
-class QByteArray;
-class QTemporaryFile;
-
-class PsiPassOne {
- int *fwt_to, *lwt_to;
- float *activation, *bias, **weight;
- int **profile;
- int seqlen;
- QTemporaryFile* matrixFile;
- QByteArray seq;
- QStringList weightFileNames;
-public:
- PsiPassOne(QTemporaryFile* matFile, const QStringList& weightFiles);
- ~PsiPassOne();
- void compute_output(void);
- void load_wts(const char *fname);
- void init(void);
- int getmtx();
- void predict();
- int runPsiPass();
-
-};
-
-
-#endif // SSPRED_AVPRED_H
-
=====================================
src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp deleted
=====================================
@@ -1,404 +0,0 @@
-/* PSIPRED2 - Neural Network Prediction of Secondary Structure */
-
-/* Copyright (C) 2000 David T. Jones - Created : January 2000 */
-/* Original Neural Network code Copyright (C) 1990 David T. Jones */
-
-/* 2nd Level Prediction Module */
-
-#include <QByteArray>
-#include <QFile>
-#include <QTextStream>
-#include <QString>
-#include <QDir>
-#include <U2Core/AppContext.h>
-#include <U2Core/AppSettings.h>
-#include <U2Core/UserApplicationsSettings.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <ctype.h>
-#include <time.h>
-
-#ifdef Q_OS_WIN
-#pragma warning(disable: 4996)
-#endif
-
-#include "sspred_hmulti.h"
-#include "sspred_net2.h"
-#include "sspred_utils.h"
-
-
-/* logistic 'squashing' function (+/- 1.0) */
-//#define logistic(x) ((REAL)1.0 / ((REAL)1.0 + (REAL)exp(-(x))))
-
-const char *rnames[] =
-{
- "ALA", "ARG", "ASN", "ASP", "CYS",
- "GLN", "GLU", "GLY", "HIS", "ILE",
- "LEU", "LYS", "MET", "PHE", "PRO",
- "SER", "THR", "TRP", "TYR", "VAL",
- "???"
-};
-
-// static char *wtfnm;
-//
-// static int nwtsum, fwt_to[TOTAL], lwt_to[TOTAL];
-// static REAL activation[TOTAL], bias[TOTAL], *weight[TOTAL];
-//
-// static float profile[MAXSEQLEN][3];
-//
-// static char seq[MAXSEQLEN];
-//
-// static int seqlen, nprof;
-
-PsiPassTwo::PsiPassTwo() {
-
- fwt_to = (int*) malloc(TOTAL*sizeof(int));
- lwt_to = (int*) malloc(TOTAL*sizeof(int));
- activation = (float*) malloc(TOTAL*sizeof(REAL));
- bias = (float*) malloc(TOTAL*sizeof(REAL));
- weight = (float**) malloc(TOTAL*sizeof(REAL*));
- nprof = 0; //must be initialized (at least for Fedora)
-};
-
-PsiPassTwo::~PsiPassTwo()
-{
-
- free(fwt_to);
- free(lwt_to);
- free(activation);
- free(bias);
- free(weight);
-}
-
-
-void PsiPassTwo::compute_output(void)
-{
- int i, j;
- REAL netinp;
-
- for (i = NUM_IN; i < TOTAL; i++)
- {
- netinp = bias[i];
-
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- netinp += activation[j] * weight[i][j];
-
- /* Trigger neuron */
- activation[i] = logistic(netinp);
- }
-}
-
-/*
- * load weights - load all link weights from a disk file
- */
-void PsiPassTwo::load_wts( const char *fname )
-{
- int i, j;
-
- QFile weightFile(fname);
- if (!weightFile.open(QIODevice::ReadOnly)) {
- fail("cannot open weights file");
- }
-
- QTextStream stream(&weightFile);
-
- /* Load input units to hidden layer weights */
- for (i = NUM_IN; i < NUM_IN + NUM_HID; i++)
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- {
- stream >> weight[i][j];
- }
-
- /* Load hidden layer to output units weights */
- for (i = NUM_IN + NUM_HID; i < TOTAL; i++)
- for (j = fwt_to[i]; j < lwt_to[i]; j++)
- {
- stream >> weight[i][j];
- }
-
- /* Load bias weights */
- for (j = NUM_IN; j < TOTAL; j++)
- {
- stream >> bias[j];
- }
-
-}
-
-void PsiPassTwo::init(void)
-{
- int i;
-
- for (i = NUM_IN; i < TOTAL; i++)
- if (!(weight[i] = (float*) calloc(TOTAL - NUM_OUT, sizeof(REAL))))
- fail("init: Out of Memory!");
-
- /* Connect input units to hidden layer */
- for (i = NUM_IN; i < NUM_IN + NUM_HID; i++)
- {
- fwt_to[i] = 0;
- lwt_to[i] = NUM_IN;
- }
-
- /* Connect hidden units to output layer */
- for (i = NUM_IN + NUM_HID; i < TOTAL; i++)
- {
- fwt_to[i] = NUM_IN;
- lwt_to[i] = NUM_IN + NUM_HID;
- }
-}
-
-/* Main prediction routine */
-QByteArray PsiPassTwo::predict( int niters, float dca, float dcb, const char *outname )
-{
- // char pred, predsst[MAXSEQLEN], lastpreds[MAXSEQLEN], *che = "CHE";
- // float score_c[MAXSEQLEN], score_h[MAXSEQLEN], score_e[MAXSEQLEN], bestsc, score, conf[MAXSEQLEN], predq3, av_c, av_h, av_e;
- // int aa, a, b, nb, i, j, k, n, winpos;
-
- int aa,b, nb, i, j, winpos;
- char pred, *predsst, *lastpreds;
- float *score_c, *score_h, *score_e, *conf, av_c, av_h, av_e;
-
- // Allocate buffers
- predsst = (char*) malloc(seqlen*sizeof(char));
- lastpreds = (char*) malloc(seqlen*sizeof(char));
- score_c = (float*) malloc(seqlen*sizeof(float));
- score_h = (float*) malloc(seqlen*sizeof(float));
- score_e = (float*) malloc(seqlen*sizeof(float));
- conf = (float*) malloc(seqlen*sizeof(float));
-
- FILE *ofp;
-
- ofp = fopen(outname, "w");
- if (!ofp)
- fail("Cannot open output file!");
-
- fputs("# PSIPRED VFORMAT (PSIPRED V2.6 by David Jones)\n\n", ofp);
-
- if (niters < 1)
- niters = 1;
-
- do {
- memcpy(lastpreds, predsst, seqlen);
- av_c = av_h = av_e = 0.0;
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- av_c += profile[winpos][0];
- av_h += profile[winpos][1];
- av_e += profile[winpos][2];
- }
- av_c /= seqlen;
- av_h /= seqlen;
- av_e /= seqlen;
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- for (j = 0; j < NUM_IN; j++)
- activation[j] = 0.0;
- activation[(WINR - WINL + 1) * IPERGRP] = av_c;
- activation[(WINR - WINL + 1) * IPERGRP + 1] = av_h;
- activation[(WINR - WINL + 1) * IPERGRP + 2] = av_e;
- activation[(WINR - WINL + 1) * IPERGRP + 3] = logistic((seqlen-150)/100.0);
- for (j = WINL; j <= WINR; j++)
- {
- if (j + winpos >= 0 && j + winpos < seqlen)
- {
- for (aa = 0; aa < 3; aa++)
- activation[(j - WINL) * IPERGRP + aa] = profile[j + winpos][aa];
- }
- else
- activation[(j - WINL) * IPERGRP + 3] = 1.0;
- }
- compute_output();
- if (activation[TOTAL - NUM_OUT] > (dca * activation[TOTAL - NUM_OUT + 1]) && activation[TOTAL - NUM_OUT] > (dcb * activation[TOTAL - NUM_OUT + 2]))
- pred = 'C';
- else if (dca * activation[TOTAL - NUM_OUT + 1] > activation[TOTAL - NUM_OUT] && dca*activation[TOTAL - NUM_OUT + 1] > dcb * activation[TOTAL - NUM_OUT + 2])
- pred = 'H';
- else
- pred = 'E';
- predsst[winpos] = pred;
- score_c[winpos] = activation[TOTAL - NUM_OUT];
- score_h[winpos] = activation[TOTAL - NUM_OUT + 1];
- score_e[winpos] = activation[TOTAL - NUM_OUT + 2];
- }
-
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- profile[winpos][0] = score_c[winpos];
- profile[winpos][1] = score_h[winpos];
- profile[winpos][2] = score_e[winpos];
- }
- } while (memcmp(predsst, lastpreds, seqlen) && --niters);
-
- for (winpos = 0; winpos < seqlen; winpos++)
- conf[winpos] = (2*MAX(MAX(score_c[winpos], score_h[winpos]), score_e[winpos])-(score_c[winpos]+score_h[winpos]+score_e[winpos])+MIN(MIN(score_c[winpos], score_h[winpos]), score_e[winpos]));
-
- for (winpos = 0; winpos < seqlen; winpos++)
- if (winpos && winpos < seqlen - 1 && predsst[winpos - 1] == predsst[winpos + 1] && conf[winpos] < 0.5*(conf[winpos-1]+conf[winpos+1]))
- predsst[winpos] = predsst[winpos - 1];
-
- for (winpos = 0; winpos < seqlen; winpos++)
- {
- if (winpos && winpos < seqlen - 1 && predsst[winpos - 1] == 'C' && predsst[winpos] != predsst[winpos + 1])
- predsst[winpos] = 'C';
- if (winpos && winpos < seqlen - 1 && predsst[winpos + 1] == 'C' && predsst[winpos] != predsst[winpos - 1])
- predsst[winpos] = 'C';
- }
-
- for (winpos=0; winpos<seqlen; winpos++)
- fprintf(ofp, "%4d %c %c %6.3f %6.3f %6.3f\n", winpos + 1, seq[winpos], predsst[winpos], score_c[winpos], score_h[winpos], score_e[winpos]);
-
- fclose(ofp);
-
-// FILE* pFile = fopen( "header.out", "w" );
-// if (!pFile)
-// {
-// fail("open file for writing failed");
-// }
- QByteArray result;
- nb = seqlen / 60 + 1;
- j = 1;
- for (b = 0; b < nb; b++)
- {
- //fprintf(pFile, "\nConf: ");
- for (i = 0; i < 60; i++)
- {
- if (b * 60 + i >= seqlen)
- break;
- j = b * 60 + i + 1;
- // putc(MIN((char)(10.0*conf[j-1]+'0'), '9'), pFile);
- }
-
- //fprintf("\nPred: ");
-
- for (i = 0; i < 60; i++)
- {
- if (b * 60 + i >= seqlen)
- break;
- j = b * 60 + i + 1;
- // putc(predsst[j - 1], pFile);
- result.append(predsst[j-1]);
- }
-
- //fprintf(pFile, "\n AA: ");
-
- for (i = 0; i < 60; i++)
- {
- if (b * 60 + i >= seqlen)
- break;
- j = b * 60 + i + 1;
- // putc(seq[j - 1], pFile);
-
- }
-
-// fprintf(pFile, "\n ");
-
- for (i = 0; i < 58; i++)
- {
- if (b * 60 + i + 3 > seqlen)
- break;
- j = b * 60 + i + 3;
- if (!(j % 10)) {
- // fprintf(pFile, "%3d", j);
- i += 2;
- }
- else {
- // fprintf(pFile, " ");
- }
- }
- // putc('\n', pFile);
-
- // putc('\n', pFile);
- }
-
- //fclose(pFile);
-
- //Deallocate buffers
- free(predsst);
- free(lastpreds);
- free(score_c);
- free(score_h);
- free(score_e);
- free(conf);
-
- return result;
-}
-
-/* Read PSI AA frequency data */
-int PsiPassTwo::getss(FILE * lfil)
-{
- int naa;
- float pv[3];
- char buf[256];
-
- naa = 0;
- while (!feof(lfil))
- {
- if (!fgets(buf, 255, lfil))
- break;
- seq[naa] = buf[5];
- //char c = buf[5];
- //seq.insert(naa, c);
- if (sscanf(buf + 11, "%f%f%f", &pv[0], &pv[1], &pv[2]) != 3)
- break;
-
- if (!nprof)
- {
- profile[naa][0] = pv[0];
- profile[naa][1] = pv[1];
- profile[naa][2] = pv[2];
- }
- else
- {
- profile[naa][0] += pv[0];
- profile[naa][1] += pv[1];
- profile[naa][2] += pv[2];
- }
-
- naa++;
- }
-
- nprof++;
-
- if (!naa)
- fail("Bad format!");
-
- return naa;
-}
-
-int PsiPassTwo::runPsiPass( int argc, const char *argv[], QByteArray& result )
-{
- int i;
- FILE *ifp;
-
-
-
-
- /* malloc_debug(3); */
- if (argc < 5)
- fail("usage : psipass2 weight-file itercount DCA DCB outputfile ss-infile ...");
-
- init();
- load_wts(wtfnm = argv[1]);
- QString outputFileName=U2::AppContext::getAppSettings()->getUserAppsSettings()->getUserTemporaryDirPath() + QDir::separator() + "output.ss"; //File created at sspred_avpred.cpp in method predict
- ifp = fopen(outputFileName.toLatin1().constData(), "r");
- if (!ifp) {
- fail("failed opening file for reading");
-// exit(1);
- }
- seqlen = getss(ifp);
- fclose(ifp);
-
- for (i=0; i<seqlen; i++)
- {
- profile[i][0] /= nprof;
- profile[i][1] /= nprof;
- profile[i][2] /= nprof;
- }
-
- //puts("# PSIPRED HFORMAT (PSIPRED V2.6 by David Jones)");
- QString outputFileName2=U2::AppContext::getAppSettings()->getUserAppsSettings()->getUserTemporaryDirPath() + QDir::separator() + "output.ss2";
- result = predict(atoi(argv[2]), (float)atof(argv[3]), (float)atof(argv[4]), outputFileName2.toLatin1().constData());
-
- return 0;
-}
=====================================
src/plugins_3rdparty/psipred/src/sspred_hmulti.h deleted
=====================================
@@ -1,30 +0,0 @@
-#ifndef SSPRED_HMULTI_H
-#define SSPRED_HMULTI_H
-
-#include <QVector>
-#include <QByteArray>
-#include "ssdefs.h"
-
-class QTemporaryFile;
-
-
-class PsiPassTwo {
- const char *wtfnm;
- int *fwt_to, *lwt_to;
- REAL *activation, *bias, **weight;
- float profile[MAXSEQLEN][3];
- char seq[MAXSEQLEN];
- int seqlen, nprof;
-public:
- PsiPassTwo();
- ~PsiPassTwo();
- void compute_output(void);
- void load_wts(const char *fname);
- void init(void);
- QByteArray predict(int niters, float dca, float dcb, const char *outname);
- int getss(FILE * lfil);
- int runPsiPass(int argc, const char *argv[], QByteArray& result);
-};
-
-#endif // SSPRED_HMULTI_H
-
=====================================
src/plugins_3rdparty/psipred/src/sspred_net.h deleted
=====================================
@@ -1,12 +0,0 @@
-/* Network topology definitions for 1st level networks */
-
-#define IPERGRP (21)
-
-#define WINL (-7)
-#define WINR (7)
-
-#define NUM_IN ((WINR-WINL+1)*IPERGRP) /* number of input units */
-#define NUM_HID (75) /* number of hidden units */
-#define NUM_OUT (3) /* number of output units */
-
-#define TOTAL (NUM_IN + NUM_HID + NUM_OUT)
=====================================
src/plugins_3rdparty/psipred/src/sspred_net2.h deleted
=====================================
@@ -1,23 +0,0 @@
-#define IPERGRP (4)
-
-#define WINL (-7)
-#define WINR (7)
-
-#define NUM_IN ((WINR-WINL+1)*IPERGRP+3+1) /* number of input units */
-#define NUM_HID (55) /* number of hidden units */
-#define NUM_OUT (3) /* number of output units */
-
-#define TOTAL (NUM_IN + NUM_HID + NUM_OUT)
-
-#define OFF_VAL (0.01) /* Target OFF value */
-#define ON_VAL (0.99) /* Target ON value */
-
-#define IALPHA (0.9) /* Initial smoothing factor */
-#define ILRATE (0.001) /* Initial learning rate */
-#define RWMAX (0.03) /* Max random weight value */
-#define SAMPINTV (1) /* Sampling interval */
-#define SAMPSIZE (0) /* Samples per weight update */
-
-#define CPU_MAX (10*3600.0) /* Maximum CPU time (secs) for learning */
-
-#define noEPOCHMODE
=====================================
src/plugins_3rdparty/psipred/src/sspred_utils.cpp deleted
=====================================
@@ -1,32 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "sspred_utils.h"
-
-void err( const char *s )
-{
- fprintf(stderr, "%s\n", s);
-}
-
-void fail( const char *s )
-{
- err(s);
- throw(s); //to avoid exit
- //exit(1);
-}
-
-int aanum(int ch)
-{
-
- static const int aacvs[] =
- {
- 999, 0, 20, 4, 3, 6, 13, 7, 8, 9, 20, 11, 10, 12, 2,
- 20, 14, 5, 1, 15, 16, 20, 19, 17, 20, 18, 20
- };
-
- return (isalpha(ch) ? aacvs[ch & 31] : 20);
-}
-
-
=====================================
src/plugins_3rdparty/psipred/src/sspred_utils.h deleted
=====================================
@@ -1,23 +0,0 @@
-#ifndef SSPRED_UTILS_H
-#define SSPRED_UTILS_H
-
-class QByteArray;
-class QTemporaryFile;
-
-#define PSIPRED_ANNOTATION_NAME "psipred_results"
-
-/* Dump error message */
-void err(const char *s);
-/* Dump error message and exit */
-void fail(const char *s);
-/* Convert AA letter to numeric code (0-20) */
-int aanum(int ch);
-/* generate matrix from sequence */
-int seq2mtx(const char* seq, int length, const char* outFileName);
-/* generate matrix from sequence */
-int seq2mtx(const char* seq, int length, QTemporaryFile* tmpFile);
-
-
-
-
-#endif
View it on GitLab: https://salsa.debian.org/med-team/ugene/commit/b00eb8f9881c66353834ab6f8e49483b875c2114
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/commit/b00eb8f9881c66353834ab6f8e49483b875c2114
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